I did a bit more experimenting today. First test:

/opt/bin/pg_upgrade -d /usr/local/pgsql/data -D /usr/local/pgsql_93/data/
-b /usr/local/bin/ -B /opt/bin/ -p 5452 -P 5451

It completes successfully, however I still have the user defined
tablespaces inside the 9.0 data folder. So I manually moved all tablespaces
into the new 9.3 data directory. Then I deleted the 9.0 data directory and
renamed the 9.3 directory to /usr/local/pgsql/data. Now the tablespaces are
in the correct location and using the 9.3 data folder. The server starts up
just fine. On pgAdmin if I view the tables the data shows up, but if I do a
SELECT I get:

ERROR:  relation "sys_errors" does not exist
LINE 1: SELECT * FROM sys_errors ORDER BY created_ts DESC LIMIT 100;
                      ^
********** Error **********

ERROR: relation "sys_errors" does not exist
SQL state: 42P01
Character: 15

The second test, using the exact same pg_upgrade line. But this time I
updated the location of the tablespaces to outside the /data directory. I
updated pg_tablespace and re-created all symlinks. Now the data directory
doesn't contain the tablespaces. Again pg_upgrade completes successfully
and again I get the same error about the relation.

Any thoughts?

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