[Kde-pim] Review Request: Add indexing throttling and fixed endless indexing problems
Volker Krause
vkrause at kde.org
Mon Mar 5 15:49:15 GMT 2012
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 fast queries, so it's working in
general).
regards,
Volker
> 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/
--
Volker Krause | volker.krause at kdab.com | Senior Software Engineer
KDAB (Deutschland) GmbH&Co KG, a KDAB Group company
Tel. Germany +49-30-521325470, Sweden (HQ) +46-563-540090
KDAB - Qt Experts - Platform-independent software solutions
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