Open Microscopy Environment

by **hippogriff** » Thu Apr 14, 2016 8:08 am

I'm installing OMERO server on Windows and am having some problems.

Code: Select all: OMERO Diagnostics 5.2.2-ice35-b17 ================================================================================ Commands: java -version 1.8.0 (C:\ProgramData\Oracle\Java \javapath\java.EXE) Commands: python -V 2.7.9 (C:\Python27\python.EXE) Commands: icegridnode --version 3.5.1 (C:\Ice-3.5.1-b4-win-x64-Re lease\bin\icegridnode.EXE) Commands: icegridadmin --version 3.5.1 (C:\Ice-3.5.1-b4-win-x64-Re lease\bin\icegridadmin.EXE) Commands: psql --version 9.5.1 (C:\PostgreSQL\9.5\bin\psql .EXE)

When I use 'omero admin start', the icegridnode server does not start, but after using 'omero admin startasync' it does.

During the first few mins, Blitz-0 & DropBox both report the following:

Code: Select all: Server: icegridnode running Server: Blitz-0 activating (enabled) Server: DropBox activating (enabled) Server: FileServer active (pid = 2540, enabled) Server: Indexer-0 activating (enabled) Server: MonitorServer active (pid = 2956, enabled) Server: OMERO.Glacier2 active (pid = 3196, enabled) Server: OMERO.IceStorm active (pid = 2588, enabled) Server: PixelData-0 activating (enabled) Server: Processor-0 activating (enabled) Server: Tables-0 inactive (disabled) Server: TestDropBox inactive (enabled) Server: OMERO.master active (running as LocalSystem)

...but shortly afterwards report this:

Code: Select all: Server: icegridnode running Server: Blitz-0 inactive (disabled) Server: DropBox inactive (disabled) Server: FileServer active (pid = 2540, enabled) Server: Indexer-0 inactive (disabled) Server: MonitorServer active (pid = 2956, enabled) Server: OMERO.Glacier2 active (pid = 3196, enabled) Server: OMERO.IceStorm active (pid = 2588, enabled) Server: PixelData-0 inactive (disabled) Server: Processor-0 activating (enabled) Server: Tables-0 inactive (disabled) Server: TestDropBox inactive (enabled) Server: OMERO.master active (running as LocalSystem)

I also get this:

Code: Select all: C:\OMERO.server-5.2.2-ice35-b17\var\log>.\..\..\bin\omero login Server: [localhost:4064] Username: [Administrator] Password: internal server error

Where should I look please?

Kevin

by **jmoore** » Thu Apr 14, 2016 11:15 am

Was a var\log\Blitz-0.log file produced? Could you paste the entire diagnostics output and optimally attach a zip of the logs files if available?

Cheers,
~Josh

P.S. so that there are no surprises for you down the road, please also read http://blog.openmicroscopy.org/tech-issues/future-plans/deployment/2016/03/22/windows-support/.

by **hippogriff** » Thu Apr 14, 2016 4:30 pm

The Blitz log shows activiry at startup, but then stops. Here's an extract of the Blitz log. I don't have a database table dbpatch...not sure why I'd need one...but perhaps that fact that nothing is written to the log after startup is more telling:

Code: Select all: ******************************************************************************** ******* Error connecting to database table dbpatch. You may need to bootstrap. See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade .html ******************************************************************************** ******* at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:1 41) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.SimpleInstantiationStrategy .instantiate(SimpleInstantiationStrategy.java:107) ~[spring-beans.jar:3.0.1.RELE ASE] at org.springframework.beans.factory.support.ConstructorResolver.autowir eConstructor(ConstructorResolver.java:273) ~[spring-beans.jar:3.0.1.RELEASE] ... 25 common frames omitted Caused by: org.springframework.beans.factory.BeanCreationException: Error creati ng bean with name 'currentDetails' defined in class path resource [ome/services/ sec-primitives.xml]: Cannot resolve reference to bean 'roles' while setting cons tructor argument; nested exception is org.springframework.beans.factory.BeanCrea tionException: Error creating bean with name 'dbPatchCheck' defined in class pat h resource [ome/services/startup.xml]: Invocation of init method failed; nested exception is ome.conditions.InternalException: ******************************************************************************** ******* Error connecting to database table dbpatch. You may need to bootstrap. See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade .html ******************************************************************************** ******* at org.springframework.beans.factory.support.BeanDefinitionValueResolver .resolveReference(BeanDefinitionValueResolver.java:328) ~[spring-beans.jar:3.0.1 .RELEASE] at org.springframework.beans.factory.support.BeanDefinitionValueResolver .resolveValueIfNecessary(BeanDefinitionValueResolver.java:106) ~[spring-beans.ja r:3.0.1.RELEASE] at org.springframework.beans.factory.support.ConstructorResolver.resolve ConstructorArguments(ConstructorResolver.java:600) ~[spring-beans.jar:3.0.1.RELE ASE] at org.springframework.beans.factory.support.ConstructorResolver.autowir eConstructor(ConstructorResolver.java:140) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) ~[sprin g-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) ~[spring -beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[spring-beans .jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j ar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R ELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.getBean (AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.DefaultListableBeanFactory. preInstantiateSingletons(DefaultListableBeanFactory.java:562) ~[spring-beans.jar :3.0.1.RELEASE] at org.springframework.context.support.AbstractApplicationContext.finish BeanFactoryInitialization(AbstractApplicationContext.java:871) ~[spring-context. jar:3.0.1.RELEASE] at org.springframework.context.support.AbstractApplicationContext.refres h(AbstractApplicationContext.java:423) ~[spring-context.jar:3.0.1.RELEASE] at org.springframework.context.support.ClassPathXmlApplicationContext.<i nit>(ClassPathXmlApplicationContext.java:139) ~[spring-context.jar:3.0.1.RELEASE ] at org.springframework.context.support.ClassPathXmlApplicationContext.<i nit>(ClassPathXmlApplicationContext.java:105) ~[spring-context.jar:3.0.1.RELEASE ] at ome.system.OmeroContext.<init>(OmeroContext.java:97) ~[common.jar:na] at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_77] at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) ~[na:1.8.0_77] at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou rce) ~[na:1.8.0_77] at java.lang.reflect.Constructor.newInstance(Unknown Source) ~[na:1.8.0_ 77] at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:1 26) ~[spring-beans.jar:3.0.1.RELEASE] ... 27 common frames omitted Caused by: org.springframework.beans.factory.BeanCreationException: Error creati ng bean with name 'dbPatchCheck' defined in class path resource [ome/services/st artup.xml]: Invocation of init method failed; nested exception is ome.conditions .InternalException: ******************************************************************************** ******* Error connecting to database table dbpatch. You may need to bootstrap. See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade .html ******************************************************************************** ******* at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.initializeBean(AbstractAutowireCapableBeanFactory.java:1403) ~[spring-be ans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513) ~[spring-beans .jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j ar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R ELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.getBean (AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe an(AbstractBeanFactory.java:280) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.getBean (AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.ConstructorResolver.instant iateUsingFactoryMethod(ConstructorResolver.java:344) ~[spring-beans.jar:3.0.1.RE LEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:96 4) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:870) ~[spring -beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[spring-beans .jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j ar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R ELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.getBean (AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.BeanDefinitionValueResolver .resolveReference(BeanDefinitionValueResolver.java:322) ~[spring-beans.jar:3.0.1 .RELEASE] ... 49 common frames omitted Caused by: ome.conditions.InternalException: ******************************************************************************** ******* Error connecting to database table dbpatch. You may need to bootstrap. See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade .html ******************************************************************************** ******* at ome.services.util.DBPatchCheck.start(DBPatchCheck.java:60) ~[server.j ar:na] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8. 0_77] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8. 0_77] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na: 1.8.0_77] at java.lang.reflect.Method.invoke(Unknown Source) ~[na:1.8.0_77] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1527) ~[s pring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1468) ~[spring -beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400) ~[spring-be ans.jar:3.0.1.RELEASE] ... 67 common frames omitted

Here's the diag:

Code: Select all: C:\OMERO.server-5.2.2-ice35-b17\bin>omero admin diagnostics ================================================================================ OMERO Diagnostics 5.2.2-ice35-b17 ================================================================================ Commands: java -version 1.8.0 (C:\ProgramData\Oracle\Java \javapath\java.EXE) Commands: python -V 2.7.9 (C:\Python27\python.EXE) Commands: icegridnode --version 3.5.1 (C:\Ice-3.5.1-b4-win-x64-Re lease\bin\icegridnode.EXE) Commands: icegridadmin --version 3.5.1 (C:\Ice-3.5.1-b4-win-x64-Re lease\bin\icegridadmin.EXE) Commands: psql --version 9.5.1 (C:\PostgreSQL\9.5\bin\psql .EXE) Server: icegridnode running Server: Blitz-0 inactive (disabled) Server: DropBox inactive (disabled) Server: FileServer active (pid = 1996, enabled) Server: Indexer-0 inactive (disabled) Server: MonitorServer active (pid = 2028, enabled) Server: OMERO.Glacier2 active (pid = 1204, enabled) Server: OMERO.IceStorm active (pid = 1296, enabled) Server: PixelData-0 inactive (disabled) Server: Processor-0 activating (enabled) Server: Tables-0 inactive (disabled) Server: TestDropBox inactive (enabled) Server: OMERO.master active (running as LocalSystem) Log dir: C:\OMERO.server-5.2.2-ice35-b17\var\log exists Log files: Blitz-0.log 659.0 KB errors=332 warnings=0 Log files: DropBox.log 20.0 KB errors=26 warnings=13 Log files: FileServer.log 4.0 KB Log files: Indexer-0.log 661.0 KB errors=430 warnings=0 Log files: MonitorServer.log 4.0 KB Log files: OMEROweb.log 226.0 KB errors=96 warnings=29 Log files: OMEROweb_brokenrequest.log 0.0 KB Log files: PixelData-0.log 661.0 KB errors=430 warnings=0 Log files: Processor-0.log 3.0 MB errors=2081 warnings=10 39 Log files: Processor-0.log.1 4.0 MB errors=2824 warnings=14 12 Log files: Tables-0.log n/a Log files: TestDropBox.log n/a Log files: master.err 0.0 KB Log files: master.out 0.0 KB Log files: Total size 10.92 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:OMERO_USERDIR=(unset) Environment:OMERO_TMPDIR=(unset) Environment:PATH=C:\Python27;C:\ProgramData\Oracle\Java\javapath;C:\Windows\syst em32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v 1.0\;C:\PostgreSQL\9.5\bin;C:\Ice-3.5.1-b4-win-x64-Release\bin; Environment:PYTHONPATH=C:\Ice-3.5.1-b4-win-x64-Release\python Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO SSL port:4064 OMERO TCP port:4063 OMERO data dir:'/OMERO' Exists? True Is writable? Tru e OMERO temp dir:'C:\Users\Administrator\AppData\Roaming\omero\tmp' Exists? True Is writable? True (Size: 0) JVM settings: Blitz-${index} -Xmx2657m -XX:MaxPermSize=1g -XX:+Ig noreUnrecognizedVMOptions JVM settings: Indexer-${index} -Xmx1771m -XX:MaxPermSize=1g -XX:+Ig noreUnrecognizedVMOptions JVM settings: PixelData-${index} -Xmx2657m -XX:MaxPermSize=1g -XX:+Ig noreUnrecognizedVMOptions JVM settings: Repository-${index} -Xmx1771m -XX:MaxPermSize=1g -XX:+Ig noreUnrecognizedVMOptions OMERO.web status... DEVELOPMENT: You will have to kill processes by hand! Django version: 1.8.11

If this doesn't give enough clues I'll gladly upload the rest of the logs (the only active one is Processor). I'm concerned there isn't much in the way of log activity and commands such as 'pg_ctl status' and 'omero admin status' don't do much:

Code: Select all: C:\OMERO.server-5.2.2-ice35-b17\bin>omero admin status C:\OMERO.server-5.2.2-ice35-b17\bin>

Code: Select all: C:\PostgreSQL\9.5\bin>pg_ctl status C:\PostgreSQL\9.5\bin>

Here's the list of log files showing where the activity is - service startup here was at 14:02:

Code: Select all: C:\OMERO.server-5.2.2-ice35-b17\var\log>dir /o:d Volume in drive C has no label. Volume Serial Number is 8A3C-03D6 Directory of C:\OMERO.server-5.2.2-ice35-b17\var\log 22/03/2016 17:59 0 master.err 22/03/2016 17:59 0 master.out 24/03/2016 12:46 0 OMEROweb_brokenrequest.log 13/04/2016 20:43 4,999,862 Processor-0.log.1 13/04/2016 20:44 <DIR> .. 13/04/2016 20:44 <DIR> . 14/04/2016 14:02 4,243 FileServer.log 14/04/2016 14:02 4,318 MonitorServer.log 14/04/2016 14:02 659,561 Blitz-0.log 14/04/2016 14:02 661,816 PixelData-0.log 14/04/2016 14:02 661,660 Indexer-0.log 14/04/2016 14:02 20,176 DropBox.log 14/04/2016 17:05 226,881 OMEROweb.log 14/04/2016 17:24 3,682,772 Processor-0.log 12 File(s) 10,921,289 bytes 2 Dir(s) 69,836,877,824 bytes free

by **jmoore** » Thu Apr 14, 2016 6:13 pm

hippogriff wrote:...Here's an extract of the Blitz log. I don't have a database table dbpatch...not sure why I'd need one...

You'll definitely need to have all the database tables present and accessible for the OMERO server to start correctly.

...

If this doesn't give enough clues I'll gladly upload the rest of the logs (the only active one is Processor). I'm concerned there isn't much in the way of log activity and commands such as 'pg_ctl status' and 'omero admin status' don't do much

Shouldn't be necessary to upload anything else yet. Until OMERO has access to a full DB, we're stuck.

Interpolating in your configuration parameters from `bin\omero config get`, does the following work for you?

Code: Select all: psql -h ${omero.db.host} -U ${omero.db.user} ${omero.db.name} -l

from the machine that the OMERO server is running on?

Cheers,
~Josh.

by **hippogriff** » Thu Apr 14, 2016 6:32 pm

Thanks Josh...Here's the result:

Code: Select all: C:\PostgreSQL\9.5\bin>psql -h localhost -U omero -d omero -l Password for user omero: List of databases Name | Owner | Encoding | Collate | Ctype | Access privileges -----------+----------+----------+----------------------------+----------------------------+----------------------- omero | postgres | UTF8 | English_United States.1252 | English_United States.1252 | postgres | postgres | UTF8 | English_United States.1252 | English_United States.1252 | template0 | postgres | UTF8 | English_United States.1252 | English_United States.1252 | =c/postgres + | | | | | postgres=CTc/postgres template1 | postgres | UTF8 | English_United States.1252 | English_United States.1252 | =c/postgres + | | | | | postgres=CTc/postgres (4 rows)

by **jmoore** » Thu Apr 14, 2016 7:19 pm

Hi Hippogriff,

the owner of the DB is "postgres". This is likely the root of your problem if you are connecting to the DB as the user "omero".

Cheers,
~Josh.

by **hippogriff** » Fri Apr 15, 2016 5:42 pm

Thanks for spotting that...I've set omero to use the postgres user which owns the 'omero' db, and shut things down and rebooted server.

Here's the db connection output:

Code: Select all: C:\OMERO.server-5.2.2-ice35-b17\bin>psql -h localhost -U postgres -d omero -l Password for user postgres: List of databases Name | Owner | Encoding | Collate | Ctype | Access privileges -----------+----------+----------+----------------------------+----------------- -----------+----------------------- omero | postgres | UTF8 | English_United States.1252 | English_United S tates.1252 | postgres | postgres | UTF8 | English_United States.1252 | English_United S tates.1252 | template0 | postgres | UTF8 | English_United States.1252 | English_United S tates.1252 | =c/postgres + | | | | | postgres=CTc/postgres template1 | postgres | UTF8 | English_United States.1252 | English_United S tates.1252 | =c/postgres + | | | | | postgres=CTc/postgres (4 rows)

I've got a different error...icegridnode fails to start:

Code: Select all: C:\OMERO.server-5.2.2-ice35-b17\bin>omero admin start Found default value: c:\omero_dist\var\master Attempting to correct... Converting from c:\omero_dist to C:\OMERO.server-5.2.2-ice35-b17 Changes made: 6 No descriptor given. Using etc\grid\windefault.xml Installing OMERO.master Windows service. Successfully installed OMERO.master Windows service. Starting OMERO.master Windows service. Waiting on startup. Use CTRL-C to exit ............................. Failed to startup some components after 300 seconds Calling "stop" on remaining components OMERO.master service deleted. Waiting on shutdown. Use CTRL-C to exit ...... C:\OMERO.server-5.2.2-ice35-b17\bin>

Here are the diags:

Code: Select all: C:\OMERO.server-5.2.2-ice35-b17\bin>omero admin diagnostics ================================================================================ OMERO Diagnostics 5.2.2-ice35-b17 ================================================================================ Commands: java -version 1.8.0 (C:\ProgramData\Oracle\Java \javapath\java.EXE) Commands: python -V 2.7.9 (C:\Python27\python.EXE) Commands: icegridnode --version 3.5.1 (C:\Ice-3.5.1-b4-win-x64-Re lease\bin\icegridnode.EXE) Commands: icegridadmin --version 3.5.1 (C:\Ice-3.5.1-b4-win-x64-Re lease\bin\icegridadmin.EXE) Commands: psql --version 9.5.1 (C:\PostgreSQL\9.5\bin\psql .EXE) Server: icegridnode not started Log dir: C:\OMERO.server-5.2.2-ice35-b17\var\log exists Log files: Blitz-0.log 730.0 KB errors=372 warnings=0 Log files: DropBox.log 23.0 KB errors=30 warnings=15 Log files: FileServer.log 5.0 KB Log files: Indexer-0.log 692.0 KB errors=450 warnings=0 Log files: MonitorServer.log 5.0 KB Log files: OMEROweb.log 333.0 KB errors=106 warnings=35 Log files: OMEROweb_brokenrequest.log 0.0 KB Log files: PixelData-0.log 692.0 KB errors=450 warnings=0 Log files: Processor-0.log 1.0 MB errors=888 warnings=44 3 Log files: Processor-0.log.1 4.0 MB errors=2829 warnings=14 14 Log files: Processor-0.log.2 4.0 MB errors=2824 warnings=14 12 Log files: Tables-0.log n/a Log files: TestDropBox.log n/a Log files: master.err 0.0 KB Log files: master.out 0.0 KB Log files: Total size 14.05 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:OMERO_USERDIR=(unset) Environment:OMERO_TMPDIR=(unset) Environment:PATH=C:\Python27;C:\ProgramData\Oracle\Java\javapath;C:\Windows\syst em32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v 1.0\;C:\PostgreSQL\9.5\bin;C:\Ice-3.5.1-b4-win-x64-Release\bin; Environment:PYTHONPATH=C:\Ice-3.5.1-b4-win-x64-Release\python Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) Cannot list deployed applications. OMERO data dir:'/OMERO' Exists? True Is writable? Tru e OMERO temp dir:'C:\Users\Administrator\AppData\Roaming\omero\tmp' Exists? True Is writable? True (Size: 0) JVM settings: Blitz-${index} -Xmx2657m -XX:MaxPermSize=1g -XX:+Ig noreUnrecognizedVMOptions JVM settings: Indexer-${index} -Xmx1771m -XX:MaxPermSize=1g -XX:+Ig noreUnrecognizedVMOptions JVM settings: PixelData-${index} -Xmx2657m -XX:MaxPermSize=1g -XX:+Ig noreUnrecognizedVMOptions JVM settings: Repository-${index} -Xmx1771m -XX:MaxPermSize=1g -XX:+Ig noreUnrecognizedVMOptions OMERO.web status... DEVELOPMENT: You will have to kill processes by hand! Django version: 1.8.11

If you have any suggestions, I'd be very grateful.

by **jmoore** » Mon Apr 18, 2016 5:43 am

Code: Select all: Log files: Blitz-0.log 730.0 KB errors=372 warnings=0

Knowing the latest error from the Blitz-0.log file would be helpful. You can also zip the file and upload it if you'd rather.

All the best,
~Josh

by **hippogriff** » Mon Apr 18, 2016 4:32 pm

Here is the last x lines of the Blitz log - there are repeating messages. If this isn't sufficient info, let me know and I'll zip upload the whole thing:

Code: Select all: Caused by: org.springframework.beans.factory.BeanCreationException: Error creati ng bean with name 'dbPatchCheck' defined in class path resource [ome/services/st artup.xml]: Invocation of init method failed; nested exception is ome.conditions .InternalException: ******************************************************************************** ******* Error connecting to database table dbpatch. You may need to bootstrap. See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade .html ******************************************************************************** ******* at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.initializeBean(AbstractAutowireCapableBeanFactory.java:1403) ~[spring-be ans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513) ~[spring-beans .jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j ar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R ELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.getBean (AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe an(AbstractBeanFactory.java:280) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.getBean (AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.ConstructorResolver.instant iateUsingFactoryMethod(ConstructorResolver.java:344) ~[spring-beans.jar:3.0.1.RE LEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:96 4) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:870) ~[spring -beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[spring-beans .jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[spring-beans.j ar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory$1.getOb ject(AbstractBeanFactory.java:290) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.DefaultSingletonBeanRegistr y.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[spring-beans.jar:3.0.1.R ELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBe an(AbstractBeanFactory.java:287) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractBeanFactory.getBean (AbstractBeanFactory.java:189) ~[spring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.BeanDefinitionValueResolver .resolveReference(BeanDefinitionValueResolver.java:322) ~[spring-beans.jar:3.0.1 .RELEASE] ... 49 common frames omitted Caused by: ome.conditions.InternalException: ******************************************************************************** ******* Error connecting to database table dbpatch. You may need to bootstrap. See http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-upgrade .html ******************************************************************************** ******* at ome.services.util.DBPatchCheck.start(DBPatchCheck.java:60) ~[server.j ar:na] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8. 0_77] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8. 0_77] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na: 1.8.0_77] at java.lang.reflect.Method.invoke(Unknown Source) ~[na:1.8.0_77] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1527) ~[s pring-beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1468) ~[spring -beans.jar:3.0.1.RELEASE] at org.springframework.beans.factory.support.AbstractAutowireCapableBean Factory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400) ~[spring-be ans.jar:3.0.1.RELEASE] ... 67 common frames omitted

by **jmoore** » Mon Apr 18, 2016 4:56 pm

This still seems to say that the database initialization has gone amiss. Could you give us the output of running "\d" in the psql console?

Cheers,
~Josh.

Open Microscopy Environment

internal server error

internal server error

Re: internal server error

Re: internal server error

Re: internal server error

Re: internal server error

Re: internal server error

Re: internal server error

Re: internal server error

Re: internal server error

Re: internal server error

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