[ome-users] restarting ome server(s) - mac os x
Bob Marinelli
bobm at stanford.edu
Thu May 26 19:52:51 BST 2005
Hi Ilya & Chris,
The httpd/error_log is pretty clean, for each image being imported we
get this:
[Wed May 25 15:48:57 2005] null: Use of uninitialized value in
numeric comparison (<=>) at /Library/Perl/5.8.6/OME/Tasks/
ImageManager.pm line 606.
[Wed May 25 15:48:57 2005] null: Use of uninitialized value in
numeric comparison (<=>) at /Library/Perl/5.8.6/OME/Tasks/
ImageManager.pm line 606.
[Wed May 25 15:48:57 2005] null: Use of uninitialized value in
numeric comparison (<=>) at /Library/Perl/5.8.6/OME/Tasks/
ImageManager.pm line 606.
... lots more similar lines removed ...
[Wed May 25 15:48:57 2005] null: Use of uninitialized value in string
eq at /Library/Perl/5.8.6/OME/Tasks/ImageManager.pm line 616.
[Wed May 25 15:48:57 2005] null: Use of uninitialized value in string
eq at /Library/Perl/5.8.6/OME/Tasks/ImageManager.pm line 616.
[Wed May 25 15:48:57 2005] null: Use of uninitialized value in string
eq at /Library/Perl/5.8.6/OME/Tasks/ImageManager.pm line 616.
which looks like maybe the tiff files being imported are lacking some
attribute(s)?
> My guess would be that its Postgres that hung, and not Apache -
> especially since you were not able to use 'ome top' - which doesn't
> depend on Apache, but does depend on Postgres.
ome top is still hanging:
Administrators-Computer:/Library/Perl/5.8.6/OME/Tasks bob$ ome top
Cannot login via previous session.
Please login to OME:
Username? bob
Password?
Great, you're in.
but we do have a fair number of postgres tasks in unix top:
Administrators-Computer:/Library/Perl/5.8.6/OME/Tasks bob$ ps aux|
grep post
postgres 6269 0.0 -0.1 48080 1540 p1- S 12:07PM
0:00.38 ./postmaster -D /usr/local/pgsql/data
postgres 6270 0.0 -0.0 48788 484 p1- S 12:07PM 0:00.03
postgres: stats buffer process
postgres 6271 0.0 -0.0 47800 612 p1- S 12:07PM 0:00.15
postgres: stats collector process
postgres 19604 0.0 -0.1 48336 3108 p1- S 12:57PM 0:00.35
postgres: www ome [local] idle in transaction
postgres 19606 0.0 -0.1 48064 2492 p1- S 12:57PM 0:00.06
postgres: www ome [local] DELETE
postgres 19612 0.0 -0.1 48336 3108 p1- S 1:01PM 0:00.43
postgres: www ome [local] idle in transaction
postgres 19614 0.0 -0.1 48064 2464 p1- S 1:01PM 0:00.10
postgres: www ome [local] DELETE
postgres 19631 0.0 -0.1 48336 3052 p1- S 1:08PM 0:00.21
postgres: www ome [local] idle in transaction
postgres 19632 0.0 -0.1 48064 2676 p1- S 1:08PM 0:01.28
postgres: www ome [local] idle
postgres 19743 0.0 -0.1 48336 2960 p1- S 1:41PM 0:00.10
postgres: www ome [local] idle in transaction
postgres 19744 0.0 -0.1 48080 2748 p1- S 1:41PM 0:01.17
postgres: www ome [local] UPDATE
postgres 20260 0.0 -0.2 48880 3708 ?? S 1:48PM 0:00.77
postgres: www ome [local] idle in transaction
postgres 20265 0.0 -0.1 48064 2744 ?? S 1:48PM 0:00.11
postgres: www ome [local] DELETE
postgres 20586 0.0 -0.1 48336 3080 ?? S 1:53PM 0:00.28
postgres: www ome [local] idle in transaction
postgres 20588 0.0 -0.1 48064 2428 ?? S 1:53PM 0:00.06
postgres: www ome [local] idle
postgres 20837 0.0 -0.1 48336 2888 ?? S 1:59PM 0:00.17
postgres: www ome [local] idle in transaction
postgres 20838 0.0 -0.1 48064 2412 ?? S 1:59PM 0:00.03
postgres: www ome [local] idle
postgres 20854 0.0 -0.1 48080 2468 ?? S 2:02PM 0:00.02
postgres: bob ome [local] UPDATE
postgres 20864 0.0 -0.1 48080 2468 ?? S 2:05PM 0:00.02
postgres: bob ome [local] UPDATE
postgres 20870 0.0 -0.1 48080 2468 ?? S 2:05PM 0:00.02
postgres: bob ome [local] UPDATE
postgres 20913 0.0 -0.1 48080 2472 ?? S 2:13PM 0:00.02
postgres: bob ome [local] UPDATE
postgres 21108 0.0 -0.2 48336 3156 ?? S 3:50PM 0:00.39
postgres: www ome [local] idle in transaction
postgres 21109 0.0 -0.1 48064 2412 ?? S 3:50PM 0:00.02
postgres: www ome [local] idle
postgres 21384 0.0 -0.1 48336 2996 ?? S 10:49AM 0:00.10
postgres: www ome [local] idle in transaction
postgres 21385 0.0 -0.1 48064 2440 ?? S 10:49AM 0:00.02
postgres: www ome [local] idle
> If you installed Postgres using the package we mirror, then you
> should be able to do this:
> sudo /Library/StartupItems/PostgreSQL/PostgreSQL stop
Tried this, suspect the stop command is buggy:
Administrators-Computer:/Library/Perl/5.8.6/OME/Tasks bob$ sudo /
Library/StartupItems/PostgreSQL/PostgreSQL stop
Password:
Stopping PostgreSQL database services
waiting for postmaster to shut
down................................................................
failed
pg_ctl: postmaster does not shut down
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: ??: no
such pid
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: S: no
such pid
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: 0:00.77:
no such pid
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill:
postgres:: no such pid
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: www: no
such pid
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: ome: no
such pid
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: [local]:
no such pid
...few hundred more similar lines deleted...
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: www: no
such pid
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: ome: no
such pid
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: [local]:
no such pid
/Library/StartupItems/PostgreSQL/PostgreSQL: line 61: kill: UPDATE:
no such pid
> sudo /Library/StartupItems/PostgreSQL/PostgreSQL start
Administrators-Computer:/Library/Perl/5.8.6/OME/Tasks bob$ sudo /
Library/StartupItems/PostgreSQL/PostgreSQL start
Starting PostgreSQL database server
/usr/local/bin/pg_ctl: line 335: /usr/local/pgsql/logfile: Permission
denied
postmaster successfully started
> Possibly the startup item is in /System/Library/StartupItems/
> PostgreSQL/PostgreSQL (where it really belongs).
"postmaster successfully started" is a bit optimistic:
Administrators-Computer:/Library/Perl/5.8.6/OME/Tasks bob$ ps aux|
grep post
bob 21568 0.0 -0.0 18032 300 p4 R+ 11:02AM 0:00.01
grep post
The good news is we've now line numbers to go look at :) so manually
changed ownership
of the /usr/local/pgsql directory to postgres:
Administrators-Computer:~ bob$ sudo /Library/StartupItems/PostgreSQL/
PostgreSQL start
Starting PostgreSQL database server
postmaster successfully started
Administrators-Computer:~ bob$ ps aux|grep post
postgres 21605 0.0 -0.1 38812 1572 p4 S 11:06AM
0:00.02 /usr/local/bin/postmaster -i
postgres 21606 0.0 -0.0 39520 452 p4 S 11:06AM 0:00.00
postgres: stats buffer process
postgres 21607 0.0 -0.0 38532 588 p4 S 11:06AM 0:00.00
postgres: stats collector process
Upon browsing over to http://localhost, we get this (have not seen it
before):
Error serving OME::Web::Home: DBD::Pg::db rollback failed: rollback
failed at /Library/Perl/5.8.6/OME/Factory.pm line 574.
Internal Error
And the httpd log had an exceptionally interesting set of errors. A
restart was the next
step, this cleared up things nicely. It was then possible to log in
and clear the Tasks items,
the hung tasks showed up as Failed and it was possible to clean them.
> As Chris said, we haven't done testing on Tiger, but are glad to
> see its not completely broken.
> I am curious to see what the last few hundred lines of /var/log/
> httpd/error_log has to say though.
> -Ilya
Thanks to your very quick responses, I'll keep a log of anything we
come across that looks like
a tiger-specific problem.
For today, I'll try tracking down the import failures in ImageManager.
Again, thanks very much,
Bob
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