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March 11, 2019

Question:

Why does the Columbus db fail to initialise after installing on Vanilla RHEL/CentOS 6.10 OS?

Answer:


As part of the Columbus installation process, the install script has to restart the potgreSQL db. Unfortunately the installation script does not allow sufficient time for postgres to be available before the installation of the Columbus db component, so it fails.

Although the installation completes the following error appears after the Columbus-db component is installed:

-----------------------------------

Installing : Columbus-db-2.9.0.147169-gen.x86_64 14/52

postmaster is stopped

Starting postgresql service: [ OK ]

creating postgres user Columbus

Stopping postgresql service: [ OK ]

Starting postgresql service: [ OK ]

warning: %post(Columbus-db-2.9.0.147169-gen.x86_64) scriptlet failed, exit status 2

Non-fatal POSTIN scriptlet failure in rpm package Columbus-db-2.9.0.147169-gen.x 86_64

-----------------------------------

When you come to start the Columbus services the db fails to initialise:

[root@columbusCentOS6 yum.repos.d]# service columbus start

* Starting Columbus

Database: /usr/local/PerkinElmerCTG/Columbus/etc/grid/config.xml read-only No descriptor given. Using etc/grid/default.xml Creating /usr/local/PerkinElmerCTG/Columbus/var/master Creating /usr/local/PerkinElmerCTG/Columbus/var/registry Waiting on startup. Use CTRL-C to exit ............................. Failed to startup some components after 300 seconds Calling "stop" on remaining components Waiting on shutdown. Use CTRL-C to exit ...... [FAILED]

Acc: [ OK ]

Web: [ OK ]

Celery: [ OK ]

In order to workaround the issue run the following command, which is actually an extract taken from the installation script:

$ su columbus

$ psql -U columbus omero4_4< /usr/local/PerkinElmerCTG/Columbus2.9/.inst/db/sql/omero.sql &> /tmp/dbinit.log

And then restart the Columbus services:

$ sudo /etc/init.d/columbus restart

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