[Kde-pim] Review Request: Add indexing throttling and fixed endless indexing problems
Sebastian Trueg
strueg at mandriva.com
Mon Mar 5 15:56:03 GMT 2012
I finally improved that. Am still testing but here the identification
part for the Akonadi indexing takes 1h instead of 4h for my test data!
I will report back tonight with more results.
On 03/05/2012 04:43 PM, Volker Krause wrote:
> On Sunday 26 February 2012 12:33:49 Sebastian Trueg wrote:
>> Since I am unable to reproduce this slow query - it seems that I am
>> missing data which results in such a query - could you please:
>>
>> * apply the attached patch to kde-runtime/nepomuk/services/backupsync (-p3)
>> * shutdown akonadi and nepomuk, remove the nepomuk db (or move it to a
>> backup location)
>> * start the storage service manually: "nepomukservicestub nepomukstorage
>> 2> /tmp/mytmpfile"
>> * start akonadi, let it finish its indexing, even if Virtuoso goes wild
>> * finally get the hardest query via: "grep XXXXX /tmp/mytmpfile|sed
>> "s/.*XXXXX //g"|sort -n|uniq|tail -20".
>>
>> Thanks for the help.
> 20420633 sparql select distinct ?r count(?p) as ?cnt where { ?r ?p ?o. filter(
> ?p in (<ht
> 11627450 sparql select distinct ?r count(?p) as ?cnt where { ?r ?p ?o. filter(
> ?p in (<ht
> 2 status()
> 4850172 sparql select distinct ?r count(?p) as ?cnt where { ?r ?p ?o. filter(
> ?p in (<ht
> 5972876 sparql select distinct ?r count(?p) as ?cnt where { ?r ?p ?o. filter(
> ?p in (<ht
>
> doesn't look like this is working :-(
>
> I ended up with 4 threads with infinite queries now, but no output, as they
> never finish (I see the output for the working queries, so it's working in
> general).
>
> regards,
> Volker
>
>> Cheers,
>> Sebastian
>>
>> On 02/22/2012 05:48 PM, Volker Krause wrote:
>>> Here we go:
>>>
>>> Connected to OpenLink Virtuoso
>>> Driver: 06.01.3127 OpenLink Virtuoso ODBC Driver
>>> OpenLink Interactive SQL (Virtuoso), version 0.9849b.
>>> Type HELP; for help and EXIT; to exit.
>>> SQL> status();
>>> REPORT
>>> VARCHAR
>>> __________________________________________________________________________
>>> _____
>>>
>>> OpenLink Virtuoso Server
>>> Version 06.01.3127-pthreads for Linux as of ??? ?? ????
>>> Started on: 2012/02/20 14:34 GMT+60
>>> Lite Mode
>>>
>>> Database Status:
>>> File size 1344274432, 164096 pages, 53194 free.
>>> 400 buffers, 400 used, 1 dirty 1 wired down, repl age 125 0 w. io 1
>>> w/crsr.
>>> Disk Usage: 1114387496 reads avg 0 msec, 0% r 0% w last 0 s, 8976288
>>>
>>> writes,
>>>
>>> 537880 read ahead, batch = 6. Autocompact 64288 in 40567 out, 36%
>>> saved.
>>>
>>> Gate: 770368 2nd in reads, 0 gate write waits, 0 in while read 0 busy
>>> scrap. Log =
>>> /home/vkrause/.kde/share/apps/nepomuk/repository/main/data/virtuosobackend
>>> /soprano- virtuoso.trx, 87 bytes
>>> 110879 pages have been changed since last backup (in checkpoint state)
>>> Current backup timestamp: 0x0000-0x00-0x00
>>> Last backup date: unknown
>>> Clients: 610 connects, max 38 concurrent
>>> RPC: 23159320 calls, -630 pending, 4 max until now, 0 queued, 2790 burst
>>> reads (0%), 15 second brk=18624512
>>> Checkpoint Remap 0 pages, 0 mapped back. 2383 s atomic time.
>>>
>>> DB master 164096 total 53194 free 0 remap 0 mapped back
>>>
>>> temp 256 total 249 free
>>>
>>> Lock Status: 0 deadlocks of which 0 2r1w, 71 waits,
>>>
>>> Currently 2 threads running 0 threads waiting 0 threads in vdb.
>>>
>>> Pending:
>>>
>>> Client 1111:1:-48: Account: dba, 415702328 bytes in, 240297225 bytes out,
>>> 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-43: Account: dba, 296436892 bytes in, 173661376 bytes out,
>>> 1 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 1 threads.
>>> Locks:
>>>
>>> Client 1111:1:-46: Account: dba, 292329482 bytes in, 179137713 bytes out,
>>> 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-17: Account: dba, 335589080 bytes in, 192090303 bytes out,
>>> 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-240: Account: dba, 10656 bytes in, 189180 bytes out, 0
>>> stmts. PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-41: Account: dba, 1552 bytes in, 938 bytes out, 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-579: Account: dba, 120819 bytes in, 273415 bytes out, 0
>>> stmts. PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-13: Account: dba, 419207763 bytes in, 243086156 bytes out,
>>> 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-2: Account: dba, 78053 bytes in, 3394883 bytes out, 0
>>> stmts. PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-69: Account: dba, 2564 bytes in, 80545 bytes out, 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:610: Account: dba, 204 bytes in, 255 bytes out, 1 stmts.
>>> PID: 14404, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 1 threads.
>>> Locks:
>>>
>>> Client 1111:1:-594: Account: dba, 339712 bytes in, 584087 bytes out, 0
>>> stmts. PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-44: Account: dba, 424311940 bytes in, 250861715 bytes out,
>>> 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-65: Account: dba, 5613 bytes in, 687096 bytes out, 0
>>> stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-29: Account: dba, 7329 bytes in, 108643 bytes out, 0
>>> stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-22: Account: dba, 28081 bytes in, 9393 bytes out, 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-470: Account: dba, 3257767 bytes in, 6410521 bytes out, 0
>>> stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-12: Account: dba, 323006521 bytes in, 181981840 bytes out,
>>> 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-81: Account: dba, 30386 bytes in, 401979 bytes out, 0
>>> stmts. PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-47: Account: dba, 398031874 bytes in, 233688412 bytes out,
>>> 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-45: Account: dba, 254603133 bytes in, 144263381 bytes out,
>>> 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-23: Account: dba, 372153873 bytes in, 224998663 bytes out,
>>> 0 stmts.
>>> PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-68: Account: dba, 10462 bytes in, 149481 bytes out, 0
>>> stmts. PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-253: Account: dba, 14802 bytes in, 1564724 bytes out, 0
>>> stmts. PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Client 1111:1:-67: Account: dba, 10881 bytes in, 169263 bytes out, 0
>>> stmts. PID: 24734, OS: unix, Application: unknown, IP#: 127.0.0.1
>>> Transaction status: PENDING, 0 threads.
>>> Locks:
>>>
>>> Running Statements:
>>> Time (msec) Text
>>>
>>> 96 status()
>>>
>>> 2177514 sparql select distinct ?r count(?p) as ?cnt where { ?r ?p ?o.
>>>
>>> filter( ?p in (<ht
>>>
>>>
>>> Hash indexes
>>>
>>>
>>> 159 Rows. -- 97 msec.
>>>
>>> On Monday 20 February 2012 17:34:27 Sebastian Trüg wrote:
>>>> Please reproduce the high load, then start
>>>> isql localhost:1111 dba dba
>>>> and run "status();"
>>>> and tell me the running queries.
>>>>
>>>> Thanks,
>>>> Sebastian
>>>>
>>>> On 02/20/2012 11:44 AM, Christian Mollekopf wrote:
>>>>> On Friday 17 February 2012 19.53:42 Volker Krause wrote:
>>>>>> On Friday 17 February 2012 09:00:19 Sebastian Trueg wrote:
>>>>>>>> On Feb. 16, 2012, 7:45 p.m., Christian Mollekopf wrote:
>>>>>>>>> The HighPrio Queue shouldn't ever be throttled ideally, but in view
>>>>>>>>> of
>>>>>>>>> the current problems it's definitely a reasonable approach. I didn't
>>>>>>>>> give a close look yet, but you can ship it from my side. Thanks for
>>>>>>>>> the
>>>>>>>>> patch.
>>>>>>> Currently there is no way around throttling the high prio queue. As
>>>>>>> stated
>>>>>>> above (and as you confirmed in private email) adding a new email
>>>>>>> account
>>>>>>> will result in newItem events for all the emails. That in turn will
>>>>>>> put
>>>>>>> them into the high prio queue.
>>>>>> I'm currently testing this, and it indeed seems to improve indexing
>>>>>> considerably. Without throttling in effect my system is now reliably
>>>>>> indexing hundreds of mails per minute, without getting stuck with
>>>>>> Virtuoso
>>>>>> going crazy.
>>>>> It also goes for me a lot faster, it seems it's not the merging which
>>>>> was
>>>>> the bottleneck after all. Not sure why it goes so much faster now
>>>>> though.>
>>>>>
>>>>>> I (locally) reduced the idle time limit a bit though, with the new two
>>>>>> minute setting it rarely switches to full speed here, maybe something
>>>>>> we
>>>>>> still want to tweak.
>>>>> Feel free to do so once that is committed.
>>>>>
>>>>>> I get a lot of these errors now though: "nepomukservicestub(24734)"
>>>>>> Soprano: "Invalid argument (1)":
>>>>>> "http://www.semanticdesktop.org/ontologies/2007/03/22/nmo#messageHeader
>>>>>> has
>>>>>> a max cardinality of 1. Provided 2 values -
>>>>>> <nepomuk:/res/dfc71807-249b-47e4-91c1-90e3bd940f4d>,
>>>>>> <nepomuk:/res/93266175- f423-481b-a371-2b6ed28c5dbb>. Existing - "
>>>>>>
>>>>>> This seems to be caused by emails with more than one extra header we
>>>>>> index
>>>>>> (such as List-Id), and thus triggers on basically everything in my
>>>>>> mailinglist folders. Affected emails are skipped and re-indexed at an
>>>>>> agent
>>>>>> restart (which of course fails again). Is nmo:messageHeader the right
>>>>>> property for these headers, and if yes, why does it have cardinality
>>>>>> one?
>>>>> I'm running into those too, I'll have a look at it. This might be
>>>>> related
>>>>> to a bug in the merger (will have to check again). I reduced the batch
>>>>> size to 1, in order to minimize this problem. Once that is working we
>>>>> probably want to increase the size again for performance reasons, which
>>>>> will of course affect the system load again (nepomuk will i.e. get 100
>>>>> items at a time instead of just one.)
>>>>>
>>>>> Otherwise I think we can commit that to master. I can backport it later
>>>>> when I have my other fixes in.
>>>>>
>>>>> Sebastian, can you commit this to master? Or do you want me to do it?
>>>>>
>>>>> I think I still have to store the already indexed collections in the
>>>>> config, because right now, if the initial indexing hasn't finished and
>>>>> the computer is rebooted it will still start over, meaning it will query
>>>>> for the existence of all items again. If that is fast enough that won't
>>>>> be a problem of course.
>>>>>
>>>>> The removal of items seems to be broken right now too, that's not
>>>>> related
>>>>> to the patch though.
>>>>>
>>>>> Also I'm still not sure that this is the actual cause the virtuoso going
>>>>> crazy bug, but in either case a very good improvement.
>>>>>
>>>>> Cheers,
>>>>> Christian
>>>>>
>>>>>> regards,
>>>>>> Volker
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> KDE PIM mailing list kde-pim at kde.org
>>>>>> https://mail.kde.org/mailman/listinfo/kde-pim
>>>>>> KDE PIM home page at http://pim.kde.org/
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