Hi Hugh. The part of interest in the log file is currently attached. Sorry for not attaching it in my previous email. I have reduced only to the log messages that could be of interest, in the specific time span, around "Please contact OpenLink Customer Support" message.
Yes I have changed the swappiness parameter to vm.swappiness = 10. I have not yet managed to use the debugger as the above error occurs. I will not insist on that. The status(); response has been copied and pasted as it came out in the isql-v command line. Actually, what happened in my last two tries executing the above, is that the SPARQL query executed (partially) as isql-v stopped the transaction because the "connection with the server had been lost" (or something like that). Thank you once more for your time. Kind regards, Pantelis Natsiavas 2016-07-12 14:30 GMT+03:00 Hugh Williams <hwilli...@openlinksw.com>: > Hi Pantelis, > > I don’t see the indicated attachment to your email with the virtuoso log ? > > Is that status(); command output complete as it normally should the CPU % > being consume by the server when running and apart from the status command, > I don’t see any other processes indicated as running ? > > Note you can use the Virtuoso PL Debugger to see what > procedures/statements are running on the server continuously as follows: > > $ isql 1111 dba <pwd> -D > OpenLink Interactive PL Debugger (Virtuoso). > Type EXIT to exit, HELP for help > Debug session estabilished to 1111 > DEBUG> info threads > @1111:4 in DB.DBA.test_proc1 () at 11 > DEBUG> > > See the following documentation of additional details on usage: > > http://docs.openlinksw.com/virtuoso/pldebugger.html#pldebugger > > > Also, do you have the Linux swappiness parameter set to minimise swapping > to disk which will degrade performance as detailed at: > > > http://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/VirtRDFPerformanceTuning#Linux-only%20--%20”swappiness > ” > > Best Regards > Hugh Williams > Professional Services > OpenLink Software, Inc. // http://www.openlinksw.com/ > Weblog -- http://www.openlinksw.com/blogs/ > LinkedIn -- http://www.linkedin.com/company/openlink-software/ > Twitter -- http://twitter.com/OpenLink > Google+ -- http://plus.google.com/100570109519069333827/ > Facebook -- http://www.facebook.com/OpenLinkSoftware > Universal Data Access, Integration, and Management Technology Providers > > On 7 Jul 2016, at 15:46, Pantelis Natsiavas <natsia...@gmail.com> wrote: > > Thank you Hugh for your answer. > > Virtuoso runs on a VM with 32GBytes of RAM. This VM is dedicated to the > specific virtuoso instance and hosted in cloud infrastructure. > > I have left my transaction to run until Tuesday (about 4 days !!!) and > still had no response. The VM reported 95% usage of memory but still no > response. The response in the status() command was the following: > *OpenLink Virtuoso Server* > *Version 07.20.3214-pthreads for Linux as of Oct 14 2015 * > *Started on: 2016-07-02 16:13 GMT+3* > > *Database Status:* > * File size 0, 10407936 pages, 3793820 free.* > * 2720000 buffers, 130665 used, 4 dirty 0 wired down, repl age 0 0 w. io > 0 w/crsr.* > * Disk Usage: 131941 reads avg 0 msec, 0% r 0% w last 0 s, 31533 writes > flush 4.255 MB,* > * 562 read ahead, batch = 224. Autocompact 0 in 0 out, 0% saved.* > *Gate: 388 2nd in reads, 0 gate write waits, 0 in while read 0 busy > scrap. * > *Log = /usr/local/var/lib/virtuoso/db/virtuoso.trx, 4146 bytes* > *6613693 pages have been changed since last backup (in checkpoint state)* > *Current backup timestamp: 0x0000-0x00-0x00* > *Last backup date: unknown* > *Clients: 1 connects, max 1 concurrent* > *RPC: 8 calls, 1 pending, 1 max until now, 0 queued, 0 burst reads (0%), 0 > second 0M large, 22M max* > *Checkpoint Remap 0 pages, 0 mapped back. 35 s atomic time.* > * DB master 10407936 total 3793820 free 0 remap 0 mapped back* > * temp 256 total 251 free* > > *Lock Status: 0 deadlocks of which 0 2r1w, 39 waits,* > * Currently 1 threads running 0 threads waiting 0 threads in vdb.* > *Pending:* > > *Client 1111:1:-3: Account: dba, 215 bytes in, 289 bytes out, 1 stmts.* > *PID: 30445, OS: unix, Application: unknown, IP#: 127.0.0.1* > *Transaction status: PENDING, 1 threads.* > *Locks: * > > > *Running Statements:* > * Time (msec) Text* > * 567 status()* > > > *Hash indexes* > > > On Wednesday, I restarted the VM in order to make sure that the > transaction was cleared, and executed the query through the isql-v while > enabling log. The usage of memory is currently about 60% and I got plenty > of log messages that I cannot really interpret. I attach the log file in > the current email. Perhaps, you could provide me with some guidance on what > I should do, based on the log file. > > Please note the following: > > The values in the virtuoso.ini configuration file are: > > *NumberOfBuffers = 2720000* > *MaxDirtyBuffers = 2000000* > > The response in the status(); command in the SQL is the following: > > *OpenLink Virtuoso Server* > *Version 07.20.3214-pthreads for Linux as of Oct 14 2015 * > *Started on: 2016-07-06 20:17 GMT+3* > > *Database Status:* > * File size 0, 11027968 pages, 3947693 free.* > * 2720000 buffers, 483125 used, 31 dirty 0 wired down, repl age 0 0 w. io > 0 w/crsr.* > * Disk Usage: 472040 reads avg 0 msec, 0% r 0% w last 0 s, 936646 writes > flush 10.35 MB,* > * 2533 read ahead, batch = 168. Autocompact 530282 in 446316 out, 15% > saved col ac: 45742 in 12% saved.* > *Gate: 446 2nd in reads, 0 gate write waits, 0 in while read 0 busy > scrap. * > *Log = /usr/local/var/lib/virtuoso/db/virtuoso.trx, 1403 bytes* > *7079218 pages have been changed since last backup (in checkpoint state)* > *Current backup timestamp: 0x0000-0x00-0x00* > *Last backup date: unknown* > *Clients: 1 connects, max 1 concurrent* > *RPC: 6 calls, 1 pending, 1 max until now, 0 queued, 0 burst reads (0%), 0 > second 0M large, 152M max* > *Checkpoint Remap 589 pages, 0 mapped back. 464 s atomic time.* > * DB master 11027968 total 3947693 free 589 remap 2 mapped back* > * temp 256 total 251 free* > > *Lock Status: 0 deadlocks of which 0 2r1w, 20 waits,* > * Currently 1 threads running 0 threads waiting 0 threads in vdb.* > *Pending:* > > *Client 1111:1:-2: Account: dba, 215 bytes in, 289 bytes out, 1 stmts.* > *PID: 10273, OS: unix, Application: unknown, IP#: 127.0.0.1* > *Transaction status: PENDING, 1 threads.* > *Locks: * > > > *Running Statements:* > * Time (msec) Text* > * 673 status()* > > > *Hash indexes* > > Thank you in advance for your help. > > Kind regards, > Pantelis Natsiavas > > > > > 2016-07-02 23:22 GMT+03:00 Hugh Williams <hwilli...@openlinksw.com>: > >> Hi Pantelis, >> >> SPARUL operations are performed as part of a transaction, which is stored >> in memory until the operation is completed and committed to the database, >> and for such a large graph would consume a significant amount system >> memory, possibly all available memory and not being able to complete. Thus >> how much memory is available on the system and how much is allocated for >> Virtuoso data buffers ie NumberOfBuffers INI file param and how much memory >> is left ? You can run the “status();” command from isql to see the Buffers >> setting and other Virtuoso server status metrics. >> >> You can also try prepending the query with the "DEFINE sql:log-enable 3” >> pragma which sets transaction log mode to autocommit during the insert >> significantly reducing the memory requirement which may then allow the >> operation to complete, as is required when deleting large graphs as >> documented at: >> >> >> http://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/VirtTipsAndTricksGuideDeleteLargeGraphs >> >> I also note you are running a 3214 build which is from June 2015 and >> would recommend updating to the latest 3217 build from April 2016 … >> >> Best Regards >> Hugh Williams >> Professional Services >> OpenLink Software, Inc. // http://www.openlinksw.com/ >> Weblog -- http://www.openlinksw.com/blogs/ >> LinkedIn -- http://www.linkedin.com/company/openlink-software/ >> Twitter -- http://twitter.com/OpenLink >> Google+ -- http://plus.google.com/100570109519069333827/ >> Facebook -- http://www.facebook.com/OpenLinkSoftware >> Universal Data Access, Integration, and Management Technology Providers >> >> > On 2 Jul 2016, at 15:06, Pantelis Natsiavas <natsia...@gmail.com> >> wrote: >> > >> > Hi everybody. >> > >> > I am trying to execute the following query >> > >> > INSERT INTO GRAPH <targetGraph> { >> > ?a <someProperty> ?b >> > } >> > WHERE { >> > GRAPH <sourceGraph> { >> > ?a <someOtherProperty> ?c . >> > BIND(REPLACE(STR(?a),"something:", "", "i") AS ?b) } >> > } >> > >> > The sourceGraph contains about 94 million triplets. When I execute the >> above SPARQL, I get no error, however, I get no response either. I check >> after some minutes and the <targetGraph> has not yet been created. The >> system acts as if I had never executed the statement. >> > >> > I have tried executing the above through /sparql and through the >> /conductor web interfaces. >> > >> > Is there a way to see what is really going on? Am I doing something >> wrong? >> > >> > I have also already tried to debug through the isql-v localhost:8890 >> dba <password> -D but I get a totally uncomprehensible error: >> > >> > isql-v() [0x44986a] >> > isql-v() [0x4498c8] >> > isql-v() [0x44b00e] >> > isql-v() [0x42fc65] >> > isql-v() [0x4108b0] >> > isql-v() [0x4043ee] >> > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fc06a645ec5] >> > isql-v() [0x40441e] >> > GPF: Dkernel.c:3080 can't free if in served sessions >> > Segmentation fault (core dumped) >> > >> > Please note that I am using Version: 07.20.3214, Build: Oct 14 2015 on >> ubuntu server. >> > >> > Kind regards, >> > Pantelis Natsiavas >> > >> ------------------------------------------------------------------------------ >> > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> > Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> > present their vision of the future. This family event has something for >> > everyone, including kids. Get more information and register today. >> > http://sdm.link/attshape_______________________________________________ >> > Virtuoso-users mailing list >> > Virtuoso-users@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/virtuoso-users >> >> > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape_______________________________________________ > Virtuoso-users mailing list > Virtuoso-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/virtuoso-users > > >
virtuoso.log.part
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