Hugh,I tried with the isql command line ensuring that the query is all on the same line:
SQL> explain('prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> select distinct ?ontology from <http://www.semantic-systems-biology.org/ontology/rdf/OBO> where{ ?term rdf:type ?ontology. } order by ?ontology ');
*** Error 37000: [Virtuoso Driver][Virtuoso Server]SQ074: Line 1: syntax error at 'rdf' before ':'
at line 23 of Top-Level:explain('prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> select distinct ?ontology from <http://www.semantic-systems-biology.org/ontology/rdf/OBO> where{ ?term rdf:type ?ontology. } order by ?ontology ')
SQL>I also tried with the interactive UI in one line and multiple lines. The result is the same :-(
The statement execution did not return a result set. SQLState: 37000 Message: SQ074: Line 1: syntax error at 'rdf' before ':' Erick Hugh Williams wrote:
Hi Erick,If you are executing from the isql commandl line then you most probably need to ensure the query is all on the same line as multiple lines will not be passed as one query to the server. Multiple lines would best in the Conductor Interactive SQL UI, which you could try also.Best Regards Hugh Williams Professional Services OpenLink Software On 9 Jun 2008, at 17:40, Erick Antezana wrote:Hi Hugh,I tried to run both queries (first surrounded by the 'explain' command) and I've got the following error message:The statement execution did not return a result set. SQLState: 37000 Message: SQ074: Line 1: syntax error at 'rdf' before ':' I also tried without the 'explain' command and I've got: SQLState: 22023Message: SR007: Function trim needs a string or NULL as argument 1, not an arg of type ARRAY_OF_POINTER (193)Moreover, I tried with the advanced tab and selecting the explain option and I've got:SQLState: 22023Message: SR007: Function trim needs a string or NULL as argument 1, not an arg of type ARRAY_OF_POINTER (193)From the command line (isql): SQL> explain('prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> select distinct ?ontology from <http://www.semantic-systems-biology.org/ontology/rdf/OBO> where{ ?term rdf:type ?ontology. }order by ?ontology ')Type the rest of statement, end with a semicolon (;)> Type the rest of statement, end with a semicolon (;)> Type the rest of statement, end with a semicolon (;)> Type the rest of statement, end with a semicolon (;)> Type the rest of statement, end with a semicolon (;)> Type the rest of statement, end with a semicolon (;)> ;*** Error 37000: [Virtuoso Driver][Virtuoso Server]SQ074: Line 1: syntax error at 'rdf' before ':'in lines 1-7 of Top-Level: #line 1 "(console)" explain('prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> select distinct ?ontology from <http://www.semantic-systems-biology.org/ontology/rdf/OBO> where{ ?term rdf:type ?ontology. } order by ?ontology '); Am I missing something? thanks, Erick Hugh Williams wrote:Hi Eric,We have been able to see the hangs you report with the sample queries below.Can you please provide the output of running the Virtuoso explain command against these 2 queries and provide this output. The explain command provides more details on the query execution plan with Virtuoso as detailed at:http://docs.openlinksw.com/virtuoso/fn_explain.html#(NULL <http://docs.openlinksw.com/virtuoso/fn_explain.html#%28NULL>)Note you will have to use the Virtuoso isql command or Conductor Interactive SQL UI to execute the commands which will be as follows:example 1: explain('prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> prefix obo:<http://www.semantic-systems-biology.org/ontology/rdf/OBO#> prefix goa:<http://www.semantic-systems-biology.org/ontology/rdf/GOA#>prefix uni:<http://www.semantic-systems-biology.org/ontology/rdf/UNIPROT#> prefix ncbi:<http://www.semantic-systems-biology.org/ontology/rdf/NCBI#>select ?protein ?predicate ?GO_term ?GOA_association from <http://www.semantic-systems-biology.org/ontology/rdf/OBO> from <http://www.semantic-systems-biology.org/ontology/rdf/GOA> where{ ?prot rdf:type goa:prot. ?prot obo:has_source ncbi:NCBI_471821. ?prot rdfs:label ?protein. ?Statement rdf:subject ?prot. ?Statement rdf:predicate obo:located_in. obo:located_in rdfs:label ?predicate. ?Statement rdf:object obo:GO_0005737. obo:GO_0005737 rdfs:label ?GO_term. ?Statement goa:supported_by ?GOA_association. ?GOA_association obo:has_evidence_code ?eco_id. }') example 2: explain('prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> select distinct ?ontology from <http://www.semantic-systems-biology.org/ontology/rdf/OBO> where{ ?term rdf:type ?ontology. } order by ?ontology ') Best Regards Hugh Williams Professional Services OpenLink Software On 8 Jun 2008, at 09:29, Erick Antezana wrote:Hi Hugh,sorry, I forgot to add a couple of examples. here are some examples that can be tested from:http://www.cellcycleontology.org/query/38-interactive-query/82-sparql-kbexample 1: prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> prefix obo:<http://www.semantic-systems-biology.org/ontology/rdf/OBO#> prefix goa:<http://www.semantic-systems-biology.org/ontology/rdf/GOA#>prefix uni:<http://www.semantic-systems-biology.org/ontology/rdf/UNIPROT#> prefix ncbi:<http://www.semantic-systems-biology.org/ontology/rdf/NCBI#>select ?protein ?predicate ?GO_term ?GOA_association from <http://www.semantic-systems-biology.org/ontology/rdf/OBO> from <http://www.semantic-systems-biology.org/ontology/rdf/GOA> where{ ?prot rdf:type goa:prot. ?prot obo:has_source ncbi:NCBI_471821. ?prot rdfs:label ?protein. ?Statement rdf:subject ?prot. ?Statement rdf:predicate obo:located_in. obo:located_in rdfs:label ?predicate. ?Statement rdf:object obo:GO_0005737. obo:GO_0005737 rdfs:label ?GO_term. ?Statement goa:supported_by ?GOA_association. ?GOA_association obo:has_evidence_code ?eco_id. } example 2: prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> select distinct ?ontology from <http://www.semantic-systems-biology.org/ontology/rdf/OBO> where{ ?term rdf:type ?ontology. } order by ?ontologySince I am constantly testing it, changing the config parameters and adding more data, the endpoint may be down during the night (CET) duo to the entire rebuild of the system (it is build automatically from scratch taking the latest data sources...).Thanks, Erick Hugh Williams wrote:Hi Erick,You have not provided some sample queries for which these performance issues are being encountered as requested in point 3 ?Best Regards Hugh Williams OpenLink Software On 6 Jun 2008, at 14:09, Erick Antezana wrote:Hi Hugh, here you are the 'top' output:top - 14:57:25 up 13 days, 22:52, 7 users, load average: 2.57, 1.74, 1.31Tasks: 133 total, 1 running, 132 sleeping, 0 stopped, 0 zombieCpu(s): 68.0% us, 1.7% sy, 0.0% ni, 29.8% id, 0.5% wa, 0.0% hi, 0.0% si Mem: 15901500k total, 15855120k used, 46380k free, 40364k buffers Swap: 4096564k total, 1016240k used, 3080324k free, 2951672k cachedPID USER PR NI %CPU TIME+ %MEM VIRT RES SHR S COMMAND 16990 root 16 0 279 378:08.04 75.7 12.0g 11g 8256 S virtuoso-t 1 root 16 0 0 0:00.66 0.0 4756 420 388 S init 2 root RT 0 0 0:00.21 0.0 0 0 0 S migration/0 3 root 34 19 0 0:18.19 0.0 0 0 0 S ksoftirqd/0 4 root RT 0 0 0:00.20 0.0 0 0 0 S migration/1 5 root 34 19 0 0:00.88 0.0 0 0 0 S ksoftirqd/1 6 root RT 0 0 0:00.16 0.0 0 0 0 S migration/2 7 root 34 19 0 0:01.02 0.0 0 0 0 S ksoftirqd/2 8 root RT 0 0 0:00.10 0.0 0 0 0 S migration/3 9 root 34 19 0 0:15.42 0.0 0 0 0 S ksoftirqd/3 10 root 5 -10 0 0:00.00 0.0 0 0 0 S events/0 11 root 5 -10 0 0:00.01 0.0 0 0 0 S events/1 12 root 5 -10 0 0:00.04 0.0 0 0 0 S events/2 13 root 5 -10 0 0:00.00 0.0 0 0 0 S events/3 14 root 5 -10 0 0:00.00 0.0 0 0 0 S khelper 15 root 15 -10 0 0:00.00 0.0 0 0 0 S kacpid 64 root 5 -10 0 0:00.00 0.0 0 0 0 S kblockd/0 65 root 5 -10 0 0:00.00 0.0 0 0 0 S kblockd/1 66 root 5 -10 0 0:00.00 0.0 0 0 0 S kblockd/2 67 root 5 -10 0 0:00.00 0.0 0 0 0 S kblockd/3 68 root 15 0 0 0:00.00 0.0 0 0 0 S khubd 97 root 15 0 0 1:09.28 0.0 0 0 0 S kswapd1 98 root 15 0 0 1:27.16 0.0 0 0 0 S kswapd0 99 root 5 -10 0 0:00.00 0.0 0 0 0 S aio/0the machine has 2 processors, more info: $ uname -aLinux crunch 2.6.9-67.0.15.ELsmp #1 SMP Tue Apr 22 13:58:43 EDT 2008 x86_64 x86_64 x86_64 GNU/Linuxregarding the FDsPerFile param, I deleted the entire db, so I began from scratch setting that param to 8 (initally I tried out 32, and i got a similar error as reported then I tried out 16, and the same error, then 8 and it worked). Other params:[Parameters] ServerPort = 1112 DisableUnixSocket = 1 ServerThreads = 50 CheckpointInterval = 6000 O_DIRECT = 1 NumberOfBuffers = 1250000 MaxDirtyBuffers = 1000000 CaseMode = 2 MaxStaticCursorRows = 50000 CheckpointAuditTrail = 0 AllowOSCalls = 0 SchedulerInterval = 10DirsAllowed = ., /virtuoso/data/virtuoso-opensource-full/share/virtuoso/vad, /virtuoso/data/rdf, /virtuoso/data/rdf_tc, /virtuoso/db/left, /virtuoso/db/rightTransactionAfterImageLimit = 5000000000 ThreadCleanupInterval = 0 ThreadThreshold = 10 ResourcesCleanupInterval = 0 FreeTextBatchSize = 10000000 SingleCPU = 0VADInstallDir = /virtuoso/data/virtuoso-opensource-full/share/virtuoso/vad/PrefixResultNames = 0;TraceOn = errors, compile, exec, transact, sql_send, user_log, failed_logTraceOn = errors ;MaxMemPoolSize = 0 FDsPerFile = 8 [Client] SQL_PREFETCH_ROWS = 1000 SQL_PREFETCH_BYTES = 60000 SQL_QUERY_TIMEOUT = 0 SQL_TXN_TIMEOUT = 0 [VDB] ArrayOptimization = 0 NumArrayParameters = 10 VDBDisconnectTimeout = 1000 KeepConnectionOnFixedThread = 0 [Replication] ServerName = crunch ServerEnable = 1 QueueMax = 50000 .. ErrorLogLevel = 7 FileExtend = 100000 MaxCheckpointRemap = 3000000 ... thanks, erick Hugh Williams wrote:Hi Erick, Can you please provide the following:1. The output of running the top command on the machine at the time you are running these problem queries such that we can see the CPU, I/O etc consumption2. How many hard disks and CPUs are in the machine currently 3. Some of these problem queries for analysisYour FDsPerFile has too many stripes most probably, resulting in the process running out of descriptors. We would suggest you use only one stripe per physical disk.Best Regards Hugh Williams Professional Services OpenLink Software http://www.openlinksw.com On 5 Jun 2008, at 11:33, Erick Antezana wrote:Hello,could anybody point out some doc/examples for doing some performance tuning?I have been playing (in a linux box with 16GB RAM, 1 CPU, ...) with some params (numberofbuffers, maxcheckpointremap, O_DIRECT, etc) as indicated in:http://virtuoso.openlinksw.com/wiki/main/Main/VOSScale http://docs.openlinksw.com/virtuoso/rdfperformancetuning.htmlhowever, our system is still pretty slow or even no responsive :-( whilelaunching some SPARQL queries...on the other hand, we're planing on buying a new server. Could anybodyrecommend some specs (RAM, CPU, disks, ...) so that it could"steadily/reasonably" cope with huge amounts of data (about 160GB in RDF files). Any advice for the hard disks spec (type: SCSI, ...; IO rate;...)? config (striping, ...)? thanks in advance! Erickp.s. while setting the param FDsPerFile to 16 for isntance, I've got anerror while re-starting virtuoso:12:15:54 Cannot open stripe on /virtuoso/db/right/db-seg32-2.db (24)12:15:54 Server exitingshould that param be set the first time the system is started (due tothe striping?)?------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace.It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Virtuoso-users mailing listVirtuoso-users@lists.sourceforge.net <mailto:Virtuoso-users@lists.sourceforge.net>https://lists.sourceforge.net/lists/listinfo/virtuoso-users--================================================================== Erick Antezana http://www.cellcycleontology.org PhD student Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUMer...@psb.ugent.be <mailto:er...@psb.ugent.be> http://www.psb.ugent.be/~erant==================================================================--================================================================== Erick Antezana http://www.cellcycleontology.org PhD student Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM er...@psb.ugent.be http://www.psb.ugent.be/~erant ==================================================================
-- ================================================================== Erick Antezana http://www.cellcycleontology.org PhD student Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM er...@psb.ugent.be http://www.psb.ugent.be/~erant ==================================================================
