Open Microscopy Environment

Hello everybody,

DUe to our backup strategy, I'm thinking about upgrading our Omero Server to the Mac OS 10.10 (Yosemite) release.
Does anybody have any experience about that?

Thanks Julia

Hi Julia,

Hopefully others reading this who have gone through the process will have some input too that they can share. I'd recommend being particularly careful with your PostgreSQL installation.

It seems that people who have been using the PostgreSQL shipped with OS X have been having trouble during this process, which appears to upgrade it, which they weren't expecting.

More info here: http://blog.2ndquadrant.com/ware-yosemi ... s-x-10-10/

It's safest to make sure you have a database dump, via pg_dump, as detailed on our OMERO Backup and Restore documentation here: http://www.openmicroscopy.org/site/supp ... store.html

FWIW I always use PostgreSQL installed from either the EnterpriseDB installer or Homebrew, never the version shipped with OS X.

All the best,

Kenny

Hello Kenny,

thank you a lot for your reply.
I'll do the dump of the databse for sure.
I'll see what kind of experience will expect me. At the moment the omero system is running stable.
The decision to upgrade the server is not done yet.

But soon or later it hase to be done.
I'll share the process with you.

best wishes
Julia

Hello Kenny,

I'm sorry ... I updatet the the mac OS system from 9.5 to 10.10 and I totally forgot about the postgresql issue.
I 've made a dump omerodb.dump.

So I updated to mac os 10.10 to update to omero 5.2 and the omero didn't start.
I have a dump of the sql database of the win omero web server.

Could I somehow use it to rebuild my database?
The Blitz logfile looks like:

Code: Select all

ome-www:log benjaminS$ tail -15  Blitz-0.log
Caused by: ome.conditions.InternalException:
***************************************************************************************
Error connecting to database table dbpatch. You may need to bootstrap.
See http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html
***************************************************************************************

   at ome.services.util.DBPatchCheck.start(DBPatchCheck.java:64) ~[server.jar:na]
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_55]
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_55]
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_55]
   at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_55]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1527) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1468) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 67 common frames omitted
ome-www:log benjaminS$ tail -25  Blitz-0.log
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:964) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:870) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 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/omero5.1/sysadmins/server-upgrade.html
***************************************************************************************

   at ome.services.util.DBPatchCheck.start(DBPatchCheck.java:64) ~[server.jar:na]
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_55]
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_55]
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_55]
   at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_55]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1527) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1468) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 67 common frames omitted
ome-www:log benjaminS$


the omero config looks like:

Code: Select all

omero.data.dir=/Volumes/Drobo_Ex02/OMERO_DATA_PIC/
omero.db.name=omeroDB
omero.db.pass=*************
omero.db.user=omeroDBuser
omero.web.application_server=development
omero.web.debug=True

and the omero admin diagnostics looks like:

Code: Select all

ome-www:bin benjaminS$ omero admin diagnostics

================================================================================
OMERO Diagnostics 5.1.4-ice35
================================================================================
       
Commands:   java -version                  1.7.0     (/usr/bin/java)
Commands:   python -V                      2.7.7     (/usr/local/bin/python -- 2 others)
Commands:   icegridnode --version          3.5.1     (/usr/local/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/local/bin/icegridadmin)
Commands:   psql --version                 9.3.4     (/usr/local/bin/psql)

Server:     icegridnode                    not started

Log dir:    /usr/local/Cellar/omero/5.1.4/var/log exists

Log files:  Blitz-0.log                    98.0 MB       errors=602  warnings=93 
Log files:  Blitz-0.log.1                  524.0 MB      errors=2244 warnings=4632
Log files:  DropBox.log                    24.0 KB       errors=20   warnings=10 
Log files:  FileServer.log                 2.0 KB       
Log files:  Indexer-0.log                  4.0 MB        errors=8    warnings=24 
Log files:  MonitorServer.log              8.0 KB        errors=12   warnings=0   
Log files:  OMEROweb.lock                  0.0 KB       
Log files:  OMEROweb.log                   44.0 KB     
Log files:  OMEROweb_brokenrequest.lock    0.0 KB       
Log files:  OMEROweb_brokenrequest.log     0.0 KB       
Log files:  PixelData-0.log                1.0 MB        errors=0    warnings=15 
Log files:  Processor-0.log                4.0 MB        errors=1118 warnings=12 
Log files:  Processor-0.log.1              4.0 MB        errors=1409 warnings=2   
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     177.0 KB      errors=8    warnings=156
Log files:  master.out                     0.0 KB       
Log files:  Total size                     637.84 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
Environment:PYTHONPATH=(unset)             
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)     

Cannot list deployed applications.
OMERO data dir:'/Volumes/Drobo_Ex02/OMERO_DATA_PIC/' Exists? True   Is writable? True
OMERO temp dir:'/Users/benjaminS/omero/tmp'   Exists? True   Is writable? True   (Size: 18444)

JVM settings: Blitz                         -Xmx2576m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer                       -Xmx1717m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Pixeldata                     -Xmx2576m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository                    -Xmx1717m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... DEVELOPMENT: You will have to check status by hand!

Many thanks Julia
And I'm really sorry for bothering you guys...

Hi Julia,

the error you pasted suggests a mismatch between the database version and the server version. You mentioned that you updated to OMERO 5.2.0 but your diagnostics output reports 5.1.4.
Did you run the database upgrade SQL script on the restored database? To check which version is in your database, you should be able to interrogate it as follows:

Code: Select all

$ psql -U omeroDBuser omeroDB -c "select currentversion, currentpatch from dbpatch;"


Best,
Sebastien

Hi Sebastian,

I'm sorry i didn't upgrade to 5.2 yet. It is my plan to do it immediately after omero 5.1.4 is running on mac 10.10.

the patch version is:
ome-www:5.1.4 benjaminS$ grep ^omero.db.patch= etc/omero.properties
omero.db.patch=1

and in the omero.properties i could find:
omero.db.version=OMERO5.1

and the output is:
psql -U omeroDBuser omeroDB -c "select currentversion, currentpatch from dbpatch;"
psql: could not connect to server: No such file or directory
Is the server running locally and accepting
connections on Unix domain socket "/tmp/.s.PGSQL.5432"?


I've found that the TCP ports are not set.
They should look like this:
OMERO SSL port:4064
OMERO TCP port:4063
but they are missing!

Thanks Julia

Julia, if http://stackoverflow.com/questions/1247 ... -directory doesn;t help, try to reinstall postgres locally. Based on my own experience upgrading Mac OS X wipe all custom paths.

Ola

Dear Ola, dear Sebastian,
thank you a lot for your support.
I've read your recommended pages and i've found an other blog here:
http://blog.cynthiakiser.com/blog/2014/ ... -yosemite/

How did it work?
I've checked for missing empty directories pg_tblspc, pg_twophase, and pg_stat_tmp in /usr/local/var/postgres
1) brew doctor -> it tells you to update ect..
2) brew update -> the Formula has to be updated in the /usr/local/Library/Formula
3) brew doctor -> i did it a second time, at this point it told me to update xQuartz
4) create the missing directories
mkdir /usr/local/var/postgres/pg_tblspc
mkdir /usr/local/var/postgres/pg_twophase
mkdir /usr/local/var/postgres/pg_stat_tmp
when i started the psql service with: postgres -D/usr/local/var/postgres
I got a error message that, lock file "postmaster.pid" already exists and the hint: is another postmaster PID 17679 running in data directory /usr/local/var/postgres?
I just started the omero server
5) omero admin start
and omero (5.1.4) is running.
Thanks Julia