dhis2-devs team mailing list archive

[Knut Staring <knutst@xxxxxxxxx>]

Good - and you'll be happy to know that 2.17 is just around the corner ;-)

On Thu, Oct 9, 2014 at 7:48 AM, Timothy Harding <hardingt@xxxxxxxxx> wrote:

> Well, we've got some good news as I got it to work, my steps below:
> *0. Clean out  the db*
> 1. Import 2.14 DHIS2 database
> 2. Reset Ownership to 'dhis' user
> 3. Run 2.15 upgrade script
> 4. Cascade drop the patientidentifiertype table
> 5. Boot up 2.15
> 6. Shutdown 2.15, replace with 2.16
> 7. Boot up 2.16
>
> We are done with this saga for the time being. Thanks Bob and Jason for
> all the help :)! Now to start poking around in 2.16.
>
>
> Timothy Harding
> PeaceCorps Volunteer
> Republic of Vanuatu
> hardingt@xxxxxxxxx
> +678 5955137
>
> On Thu, Oct 9, 2014 at 12:01 PM, Timothy Harding <hardingt@xxxxxxxxx>
> wrote:
>
>> Thanks Jason for the direction, let me give that a shot.
>>
>> So I've just enabled logging inside the postgres.conf and looks like I
>> may have found it here:
>> 2014-10-09 11:28:31 VUT ERROR:  cannot drop table patientidentifiertype
>> because other objects depend on it
>> 2014-10-09 11:28:31 VUT DETAIL:  constraint
>> fk_program_patientidentifiertypes_patientidentifiertypeid on table
>> program_patientidentifiertypes depends on table patientidentifiertype
>> 2014-10-09 11:28:31 VUT HINT:  Use DROP ... CASCADE to drop the dependent
>> objects too.
>> 2014-10-09 11:28:31 VUT STATEMENT:  DROP TABLE patientidentifiertype
>>
>> As an aside, stackoverflow mentioned that logging was not on by default
>> for postgres, but there* is* a 1.1MB file in my /var/log/postgres/
>> directory, so something was taking STDERR and putting into a file)
>> dhis@dhis216:/var/log/postgresql$ ls -la
>> total 1124
>> drwxrwxr-t  2 root     postgres    4096 Oct  9 11:13 .
>> drwxrwxr-x 10 root     syslog      4096 Oct  9 11:13 ..
>> -rw-------  1 postgres postgres     278 Oct  9 11:13
>> postgresql-2014-10-09_111335.log
>> -rw-r-----  1 postgres adm      1122520 Oct  9 11:13
>> postgresql-9.3-main.log
>> -rw-r-----  1 postgres adm         6537 Oct  5 06:38
>> postgresql-9.3-main.log.1
>>
>> So I'm guessing the table is: patientidentifiertype, which just needs a
>> CASCADE appending to the DROP query. Curious, I finally took a look at the
>> pastebin link and lo and behold:
>> DROP TABLE patientidentifiertype CASCADE;
>>
>> Thanks for that Jason, we are getting closer now :).
>>
>> Sadly, it seems to be hanging on something else now (still Step 7), the
>> last lines from the log file (attached) are:
>> 2014-10-09 11:50:36 VUT ERROR:  column "groupby" of relation
>> "trackedentityattribute" does not exist
>> 2014-10-09 11:50:36 VUT STATEMENT:  ALTER TABLE trackedentityattribute
>> DROP COLUMN groupBy
>> but that may not be what is hanging, as entire log file is filled with
>> attempts to ALTER followed by 'does not exist', but trackedentity does
>> coorespond with the step:
>> * INFO  2014-10-09 11:50:35,345 Executing startup routine [7 of 14,
>> runlevel 4]: TrackedEntityTableAlteror
>> (DefaultStartupRoutineExecutor.java [localhost-startStop-1])
>>
>> Any help is appreciate, thanks again.
>>
>>
>> Timothy Harding
>> PeaceCorps Volunteer
>> Republic of Vanuatu
>> hardingt@xxxxxxxxx
>> +678 5955137
>>
>> On Wed, Oct 8, 2014 at 10:32 PM, Jason Pickering <
>> jason.p.pickering@xxxxxxxxx> wrote:
>>
>>> Hi Tim,
>>> Ah, the haze of travel. I did not see that you had already applied the
>>> upgrade script. I had a problem with your database, which others may also
>>> experience when upgrading from 2.14 to 2.16.. This error is visible if you
>>> carefully examine the postgresql logs. So, it is a good exercise to figure
>>> out where they are. I am pretty sure they show up at the default logging
>>> level, but you may also need to increase the logging level to see each
>>> query which is executed. After that, you can trawl through the logs and see
>>> what is causing the error. I will give you a hint....a table which needs to
>>> be dropped cannot due to a foreign key constraint.
>>>
>>> If you want to skip to the spoiler, I have posted some SQL here (
>>> http://pastebin.com/0UCGVhx7) which should solve your problem. :)
>>>
>>> Best regards,
>>> Jason
>>>
>>>
>>> On Wed, Oct 8, 2014 at 2:27 AM, Bob Jolliffe <bobjolliffe@xxxxxxxxx>
>>> wrote:
>>>
>>>> Hi Jason
>>>>
>>>> That looks like the same script Tim says he has applied.  Must be
>>>> something else.
>>>>
>>>> @Tim all those postgres processes represent the pool of connections
>>>> between dhis and postgres.  The pool parameters are fixed somewhere deep in
>>>> the webapp but I think you can expect the default is going between
>>>> something like 10(min) and 40(max).  Postgres is traditionally
>>>> multi-process rather than multi-threaded - a bit slower in terms of context
>>>> switching but very stable.  One crazy thread can't bring down the server
>>>> process.
>>>>
>>>> Bob
>>>>
>>>>
>>>> On 8 October 2014 01:08, Jason Pickering <jason.p.pickering@xxxxxxxxx>
>>>> wrote:
>>>>
>>>>> Hi Tim,
>>>>> You may want to look here for the necessary upgrade script.
>>>>>
>>>>>
>>>>> http://www.dhis2.org/download/resources/sql/rename-patient-to-trackedentity.sql
>>>>>
>>>>> Regards,
>>>>> Jason
>>>>>  On Oct 7, 2014 7:41 PM, "Timothy Harding" <hardingt@xxxxxxxxx> wrote:
>>>>>
>>>>>> Hello Developer's Group
>>>>>>
>>>>>> I'm now working on migrating from 2.14 to 2.16 in our test
>>>>>> environment and the startup for tomcat is hanging on step 7. I've included
>>>>>> some relevant snippets of logs below and have attached the full logs:
>>>>>>
>>>>>>    - stdout.txt = Standard out during importing the DHIS2 2.14
>>>>>>    database, running the upgrade script, and starting tomcat)
>>>>>>    - catalina.out = The tomcat log for the latest attempt to start
>>>>>>    up 2.16
>>>>>>
>>>>>> My Notes:
>>>>>> I can boot up 2.14 with the database dump without problem
>>>>>> I can boot up 2.16 with a *blank* database without problem (it
>>>>>> creates the live environment i.e. admin:district)
>>>>>> The problem occurs when I try to boot up 2.16 with the 2.14 database
>>>>>> (after I've run the 2.15 upgrade script found here:
>>>>>> http://www.dhis2.org/download/resources/sql/rename-patient-to-trackedentity.sql
>>>>>> )
>>>>>> It hangs at step 7 of 14 * INFO  2014-10-08 09:45:03,291 Executing
>>>>>> startup routine [7 of 14, runlevel 4]: TrackedEntityTableAlteror
>>>>>> (DefaultStartupRoutineExecutor.java [localhost-startStop-1])
>>>>>> The system, for having such meager hardware, is really snappy with
>>>>>> both the live version of 2.16, and our full production mirror of 2.14.
>>>>>> The com.hazelcast.util.HealthMonitor continues to function even
>>>>>> after the initialization process hangs at step 7 of 14 (as you can see in
>>>>>> catalina.out) Oct 08, 2014 10:36:58 AM
>>>>>> com.hazelcast.util.HealthMonitor
>>>>>>
>>>>>> Both Java and Postgres are using no cpu cycles after the hang, so it
>>>>>> doesn't *feel* like it is churning away at something:
>>>>>>
>>>>>>   PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+
>>>>>> COMMAND
>>>>>>  1413 dhis      20   0 1895572 570840  16532 S   1.0 44.7   1:48.39
>>>>>> java
>>>>>>   906 postgres  20   0  523944  30260  28868 S   0.0  2.4   0:00.47
>>>>>> postgres
>>>>>>   908 postgres  20   0  524704  77648  75724 S   0.0  6.1   0:01.04
>>>>>> postgres
>>>>>>   909 postgres  20   0  524140   4304   2904 S   0.0  0.3   0:00.16
>>>>>> postgres
>>>>>>   910 postgres  20   0  524140  14056  12656 S   0.0  1.1   0:00.50
>>>>>> postgres
>>>>>>   911 postgres  20   0  524980   3068   1096 S   0.0  0.2   0:00.11
>>>>>> postgres
>>>>>>   912 postgres  20   0  103712   1984    352 S   0.0  0.2   0:00.71
>>>>>> postgres
>>>>>>  1432 postgres  20   0  526508   7656   4524 S   0.0  0.6   0:00.00
>>>>>> postgres
>>>>>>  1433 postgres  20   0  529308  14604   8948 S   0.0  1.1   0:00.22
>>>>>> postgres
>>>>>>  1434 postgres  20   0  536664  46672  32832 S   0.0  3.7   0:08.00
>>>>>> postgres
>>>>>>  1904 postgres  20   0  525372   5652   3204 S   0.0  0.4   0:00.00
>>>>>> postgres
>>>>>>  1906 postgres  20   0  525256   4860   2548 S   0.0  0.4   0:00.00
>>>>>> postgres
>>>>>>  1907 postgres  20   0  525256   4856   2540 S   0.0  0.4   0:00.00
>>>>>> postgres
>>>>>>  2114 postgres  20   0  525372   5600   3192 S   0.0  0.4   0:00.00
>>>>>> postgres
>>>>>> (there are a lot of postgres processes it seems like)
>>>>>>
>>>>>> I saw some errors on startup but the notes for 2.16 says to expect a
>>>>>> few the first time. I also saw some errors when I ran the import and 2.15
>>>>>> upgrade script.
>>>>>> Database import (grep for errors)
>>>>>> ERROR:  must be owner of extension plpgsql
>>>>>>
>>>>>> Upgrade script (grep for errors)
>>>>>> ERROR:  table "patientaggregatereportmembers" does not exist
>>>>>> ERROR:  table "patienttabularreportmembers" does not exist
>>>>>> ERROR:  table "patientregistrationform_attributes" does not exist
>>>>>> ERROR:  table "patientregistrationform_fixedattributes" does not exist
>>>>>> ERROR:  table "patientregistrationform_identifiertypes" does not exist
>>>>>> ERROR:  table "patientregistrationform_attributes" does not exist
>>>>>> ERROR:  table "patientmobilesetting" does not exist
>>>>>>
>>>>>> Any ideas? Is there an upgrade script I've forgotten to run or maybe
>>>>>> a setting I've missed?
>>>>>>
>>>>>> Timothy Harding
>>>>>> PeaceCorps Volunteer
>>>>>> Republic of Vanuatu
>>>>>> hardingt@xxxxxxxxx
>>>>>> +678 5955137
>>>>>>
>>>>>> _______________________________________________
>>>>>> Mailing list: https://launchpad.net/~dhis2-devs
>>>>>> Post to     : dhis2-devs@xxxxxxxxxxxxxxxxxxx
>>>>>> Unsubscribe : https://launchpad.net/~dhis2-devs
>>>>>> More help   : https://help.launchpad.net/ListHelp
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> Mailing list: https://launchpad.net/~dhis2-devs
>>>>> Post to     : dhis2-devs@xxxxxxxxxxxxxxxxxxx
>>>>> Unsubscribe : https://launchpad.net/~dhis2-devs
>>>>> More help   : https://help.launchpad.net/ListHelp
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Jason P. Pickering
>>> email: jason.p.pickering@xxxxxxxxx
>>> tel:+46764147049
>>>
>>
>>
>
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>
>


-- 
Knut Staring
Dept. of Informatics, University of Oslo
+4791880522
Skype: knutstar
http://dhis2.org