Hi James,
Looking at your status output I see:
Clients: 143 connects, max 5 concurrent
RPC: 2032 calls, -246 pending, 1 max until now, 0 queued, 0 burst
reads (0%), 9 second brk=548294656
Checkpoint Remap 278243 pages, 0 mapped back. 2176 s atomic time.
DB master 12523008 total 4875616 free 278243 remap 73949 mapped back
temp 5376 total 5370 free
Lock Status: 5 deadlocks of which 5 2r1w, 2454 waits,
Currently 2 threads running 0 threads waiting 0 threads in vdb.
Indicating their are 5 deadlocks in the database. Can you try running
the following command form the isql command line too to try and
forcibly kill and release all transactions and locks:
txn_killall();
As detailed at:
http://docs.openlinksw.com/virtuoso/fn_txn_killall.html
Hope fully the server will then start responding again ...
Best Regards
Hugh Williams
Professional Services
OpenLink Software
Web: http://www.openlinksw.com
Support: http://support.openlinksw.com
Forums: http://boards.openlinksw.com/support
Twitter: http://twitter.com/OpenLink
On 26 Oct 2009, at 17:36, James Marsh wrote:
Using virtuoso 6-TP1, several weeks ago, I imported approx
500,000,000 triples from several bio2rdf graphs and built the
additional bitmap indices RDF_QUAD_GPOS, RDF_QUAD_OGPS,
RDF_QUAD_OPGS, RDF_QUAD_POGS
I also created a free text index using:
DB.DBA.RDF_OBJ_FT_RULE_ADD(NULL, NULL, 'bio-ft-index')
None of the RDF data have been changed since then.
I have since upgraded to the full Virtuoso 6.0 release (running on
64 bit Ubuntu Linux).
Left alone the database transaction log grows rapidly (300MB+ in 6
hours or so) and after a while it stops responding to (formerly
working) odbc queries, though isql and the web interface continue to
work fine. In this state, there are often thousands of entries in
the output of status() consisting of IEP, IER, ISP etc:
OpenLink Virtuoso Server
Version 06.00.3123-pthreads for Linux as of Oct 24 2009
Started on: 2009/10/25 16:04 GMT+00
Database Status:
File size 102588481536, 12523008 pages, 4875617 free.
400000 buffers, 399225 used, 341076 dirty 3 wired down, repl age
1055029 22129 w. io 2 w/crsr.
Disk Usage: 7468535 reads avg 10 msec, 98% r 0% w last 6 s,
9281852 writes,
1531 read ahead, batch = 319. Autocompact 1301469 in 1071895 out,
17% saved.
Gate: 43356 2nd in reads, 0 gate write waits, 0 in while read 0
busy scrap.
Log = utopia-database.trx, 326890480 bytes
1151167 pages have been changed since last backup (in checkpoint
state)
Current backup timestamp: 0x8223-0x20-0xEE
Last backup date: Thu Oct 22 11:59:12 2009
Clients: 143 connects, max 5 concurrent
RPC: 2032 calls, -246 pending, 1 max until now, 0 queued, 0 burst
reads (0%), 9 second brk=548294656
Checkpoint Remap 278243 pages, 0 mapped back. 2176 s atomic time.
DB master 12523008 total 4875616 free 278243 remap 73949 mapped back
temp 5376 total 5370 free
Lock Status: 5 deadlocks of which 5 2r1w, 2454 waits,
Currently 2 threads running 0 threads waiting 0 threads in vdb.
Pending:
6324267: ISR 0
0: ISR 0
10292114: IEP 0
11794176: ISR 0
2: IER 0
11066624: ISR 0
44: IER 0
11259136: IER 0
13: IER 0
12105985: ISR 0
134: IER 0
[... skip a lot more ISR and IER entries ... ]
Client 1111:209:-210: Account: kend, 1010 bytes in, 1404 bytes
out, 1 stmts.
PID: 5046, OS: unix, Application: unknown, IP#: 192.168.122.253
Transaction status: PENDING, 0 threads.
Locks: 9227654: IS, 159214: IS, 6324267: IS, 10771394: IS,
Client 1111:123:-124: Account: dba, 506 bytes in, 1878114 bytes out,
1 stmts.
PID: 1708, OS: unix, Application: unknown, IP#: 127.0.0.1
Transaction status: PENDING, 0 threads.
Locks:
Running Statements:
Time (msec) Text
Replication Status: Server anonymous.
anonymous anonymous 0 OFF.
Hash indexes
No. of rows in result: 2357
With tracing enabled and no external connections to the DB, and
nothing listed by status() under "Running Statements" , the
following messages are continually produced:
trace_on('user_log', 'ddl_log', 'client_sql', 'errors', 'transact',
'exec', 'thread');
16:26:31 LTRS_2 0 Internal Internal Restart transact 0x7f66bca67790
16:26:33 LTRS_1 0 Internal Internal Commit transact 0x7f66bca67790
140733193388032
16:26:33 LTRS_2 0 Internal Internal Restart transact 0x7f66bca67790
16:26:35 LTRS_1 0 Internal Internal Commit transact 0x7f66bca67790
140733193388032
16:26:35 LTRS_2 0 Internal Internal Restart transact 0x7f66bca67790
16:26:41 LTRS_1 0 Internal Internal Commit transact 0x7f66bca67790
140733193388032
16:26:41 LTRS_2 0 Internal Internal Restart transact 0x7f66bca67790
16:26:44 LTRS_1 0 Internal Internal Commit transact 0x7f66bca67790
140733193388032
16:26:44 LTRS_2 0 Internal Internal Restart transact 0x7f66bca67790
16:26:48 LTRS_1 0 Internal Internal Commit transact 0x7f66bca67790
140733193388032
16:26:48 LTRS_2 0 Internal Internal Restart transact 0x7f66bca67790
What might be causing this (updating free text search? upgrading
database format from TP1 to release?) and what would be the best
remedy?
Unfortunately I have no way of knowing if this same behaviour was
exhibited before switching to the release version from TP1.
Many thanks,
James
--
Dr. James Marsh. Research Fellow, Advanced Interfaces Group.
School of Computer Science, The University of Manchester,
Oxford Road, Manchester, UK. M13 9PL.
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