Hi Virtuoso devs,
The following queries crash the virtuoso server.
Version 07.00.3203-pthreads for Linux as of Oct 11 2013
This is a build from the develop/7 branch commit
0bc9bc2dbd846a58d47bacee60b3a236a56abd4a
In each of these cases I first turn do log_enable(0);
With the aim turn this back on afterwards log_enable(3);
Also autocheckpointing is turned off with checkpoint_interval (0);
The data is
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/taxonomy.rdf.gz.
Put into a graph.
I attached the config/ini file.
This first query (below) is the UNION 25 path query levels deep for
materializing rdfs:subClassOf relationships.
The server also crashes the same way if running the following
a few times (each time adding the result file to the server). Again with
the aim of materializing the rdfs:subClassOf relationships/
CONSTRUCT {?sub rdfs:subClassOf ?super}
FROM <http://beta.sparql.uniprot.org/taxonomy/>
WHERE {
{ ?sub rdfs:subClassOf/rdfs:subClassOf ?super}
If I try to use SPARQL update directly with this query
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
INSERT {GRAPH <http://beta.sparql.uniprot.org/taxonomy/> {?sub
rdfs:subClassOf ?super} }
FROM <http://beta.sparql.uniprot.org/taxonomy/>
WHERE {
?sub rdfs:subClassOf ?midle . ?midle rdfs:subClassOf ?super .}
I see this in the logs
11:00:13 virtuoso-t() [0x8f0bf8]
11:00:13 virtuoso-t() [0x8f0c66]
11:00:13 virtuoso-t() [0x659840]
11:00:13 virtuoso-t() [0x65df30]
11:00:13 virtuoso-t() [0x6893ee]
11:00:13 virtuoso-t(bif_rl_dp_ids+0x7c) [0x68a1ec]
11:00:13 virtuoso-t() [0x5ce525]
11:00:13 virtuoso-t() [0x5d5ca1]
11:00:13 virtuoso-t() [0x5fe49a]
11:00:13 virtuoso-t() [0x602b7c]
11:00:13 virtuoso-t() [0x5d1b46]
11:00:13 virtuoso-t() [0x5d6413]
11:00:13 virtuoso-t() [0x5fe49a]
11:00:13 virtuoso-t() [0x602b7c]
11:00:13 virtuoso-t() [0x5d1b46]
11:00:13 virtuoso-t() [0x5d6413]
11:00:13 virtuoso-t() [0x5fe49a]
11:00:13 virtuoso-t() [0x602b7c]
11:00:13 virtuoso-t() [0x5d1b46]
11:00:13 virtuoso-t() [0x5d2662]
11:00:13 virtuoso-t() [0x5d310c]
11:00:13 virtuoso-t() [0x5faca6]
11:00:13 virtuoso-t() [0x5fe85c]
11:00:13 virtuoso-t(skip_node_input+0x20b) [0x5fff6b]
11:00:13 virtuoso-t() [0x5fe3a8]
11:00:13 virtuoso-t() [0x5fe903]
11:00:13 virtuoso-t() [0x5fe3a8]
11:00:13 virtuoso-t() [0x5fe903]
11:00:13 virtuoso-t() [0x6329d9]
11:00:13 virtuoso-t() [0x5fe3a8]
11:00:13 virtuoso-t() [0x5d0353]
11:00:13 virtuoso-t() [0x5d0808]
11:00:13 virtuoso-t() [0x5d6022]
11:00:13 virtuoso-t() [0x5fe49a]
11:00:13 virtuoso-t() [0x604048]
11:00:13 virtuoso-t() [0x60bce7]
11:00:13 virtuoso-t(sf_sql_execute_w+0x7f) [0x60c30f]
11:00:13 virtuoso-t() [0x8f72de]
11:00:13 virtuoso-t() [0x8f7f3f]
11:00:13 /lib64/libpthread.so.0() [0x35e3407851]
11:00:13 /lib64/libc.so.6(clone+0x6d) [0x35e2ce890d]
11:00:13 GPF: vec.c:1181 extending dc past max batch size
GPF: vec.c:1181 extending dc past max batch size
And again virtuoso-t crashes without a trace.
Regards,
Jerven
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
CONSTRUCT {?sub rdfs:subClassOf ?super}
FROM <http://beta.sparql.uniprot.org/taxonomy/>
WHERE {
{ ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
?super}
UNION { ?sub
rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf ?super}
UNION { ?sub rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf ?super}
UNION { ?sub rdfs:subClassOf/rdfs:subClassOf ?super}}
--
-------------------------------------------------------------------
Jerven Bolleman jerven.bolle...@isb-sib.ch
SIB Swiss Institute of Bioinformatics Tel: +41 (0)22 379 58 85
CMU, rue Michel Servet 1 Fax: +41 (0)22 379 58 58
1211 Geneve 4,
Switzerland www.isb-sib.ch - www.uniprot.org
Follow us at https://twitter.com/#!/uniprot
-------------------------------------------------------------------
;
; virtuoso.ini
;
; Configuration file for the OpenLink Virtuoso VDBMS Server
;
; To learn more about this product, or any other product in our
; portfolio, please check out our web site at:
;
; http://virtuoso.openlinksw.com/
;
; or contact us at:
;
; general.informat...@openlinksw.com
;
; If you have any technical questions, please contact our support
; staff at:
;
; technical.supp...@openlinksw.com
;
; Database setup
;
[Database]
DatabaseFile =
/home/jbollema/git/expasy4j-sparql/./data/virtuoso/virtuoso.db
ErrorLogFile =
/home/jbollema/git/expasy4j-sparql/./data/virtuoso/virtuoso.log
LockFile =
/home/jbollema/git/expasy4j-sparql/./data/virtuoso/virtuoso.lck
TransactionFile =
/home/jbollema/git/expasy4j-sparql/./data/virtuoso/virtuoso.trx
xa_persistent_file =
/home/jbollema/git/expasy4j-sparql/./data/virtuoso/virtuoso.pxa
ErrorLogLevel = 7
FileExtend = 20000
MaxCheckpointRemap = 20000
Striping = 0
TempStorage = TempDatabase
[TempDatabase]
DatabaseFile =
/home/jbollema/git/expasy4j-sparql/./data/virtuoso/virtuoso-temp.db
TransactionFile =
/home/jbollema/git/expasy4j-sparql/./data/virtuoso/virtuoso-temp.trx
MaxCheckpointRemap = 2000
Striping = 0
;
; Server parameters
;
[Parameters]
ServerPort = 1112
LiteMode = 1
DisableUnixSocket = 0
DisableTcpSocket = 0
;SSLServerPort = 2111
;SSLCertificate = cert.pem
;SSLPrivateKey = pk.pem
;X509ClientVerify = 0
;X509ClientVerifyDepth = 0
;X509ClientVerifyCAFile = ca.pem
ServerThreads = 20
CheckpointInterval = 60
O_DIRECT = 1
CaseMode = 2
MaxStaticCursorRows = 5000
CheckpointAuditTrail = 0
AllowOSCalls = 0
SchedulerInterval = 10
DirsAllowed = ., /scratch/virtuoso//share/virtuoso/vad
ThreadCleanupInterval = 0
ThreadThreshold = 10
ResourcesCleanupInterval = 0
FreeTextBatchSize = 100000
SingleCPU = 0
VADInstallDir = /scratch/virtuoso//share/virtuoso/vad/
PrefixResultNames = 0
RdfFreeTextRulesSize = 100
IndexTreeMaps = 256
MaxMemPoolSize = 0
PrefixResultNames = 0
MacSpotlight = 0
IndexTreeMaps = 64
QueryLog = /tmp/virtuoso-query.log
;;
;; When running with large data sets, one should configure the Virtuoso
;; process to use between 2/3 to 3/5 of free system memory and to stripe
;; storage on all available disks.
;;
;; Uncomment next two lines if there is 2 GB system memory free
; NumberOfBuffers = 170000
; MaxDirtyBuffers = 130000
;; Uncomment next two lines if there is 4 GB system memory free
; NumberOfBuffers = 340000
; MaxDirtyBuffers = 250000
;; Uncomment next two lines if there is 8 GB system memory free
NumberOfBuffers = 680000
MaxDirtyBuffers = 500000
;; Uncomment next two lines if there is 16 GB system memory free
; NumberOfBuffers = 1360000
; MaxDirtyBuffers = 1000000
;; Uncomment next two lines if there is 32 GB system memory free
; NumberOfBuffers = 2720000
; MaxDirtyBuffers = 2000000
;; Uncomment next two lines if there is 48 GB system memory free
; NumberOfBuffers = 4000000
; MaxDirtyBuffers = 3000000
;; Uncomment next two lines if there is 64 GB system memory free
; NumberOfBuffers = 5450000
; MaxDirtyBuffers = 4000000
;;
;; Note the default settings will take very little memory
;; but will not result in very good performance
;;
;NumberOfBuffers = 10000
;MaxDirtyBuffers = 6000
MaxQueryMem = 200K
VectorSize = 100
MaxVectorSize = 10000
AdjustVectorSize = 0
[HTTPServer]
;ServerPort = 8890
;ServerRoot = /scratch/virtuoso//var/lib/virtuoso/vsp
;ServerThreads = 20
;DavRoot = DAV
;EnabledDavVSP = 0
;HTTPProxyEnabled = 0
;TempASPXDir = 0
;DefaultMailServer = localhost:25
;ServerThreads = 10
;MaxKeepAlives = 10
;KeepAliveTimeout = 10
;MaxCachedProxyConnections = 10
;ProxyConnectionCacheTimeout = 15
;HTTPThreadSize = 280000
;HttpPrintWarningsInOutput = 0
;Charset = UTF-8
;HTTPLogFile = logs/http.log
[AutoRepair]
BadParentLinks = 0
[Client]
SQL_PREFETCH_ROWS = 100
SQL_PREFETCH_BYTES = 16000
SQL_QUERY_TIMEOUT = 0
SQL_TXN_TIMEOUT = 0
;SQL_NO_CHAR_C_ESCAPE = 1
;SQL_UTF8_EXECS = 0
;SQL_NO_SYSTEM_TABLES = 0
;SQL_BINARY_TIMESTAMP = 1
;SQL_ENCRYPTION_ON_PASSWORD = -1
[VDB]
ArrayOptimization = 0
NumArrayParameters = 10
VDBDisconnectTimeout = 1000
KeepConnectionOnFixedThread = 0
[Replication]
ServerName = db-LIN-072
ServerEnable = 1
QueueMax = 50000
;
; Striping setup
;
; These parameters have only effect when Striping is set to 1 in the
; [Database] section, in which case the DatabaseFile parameter is ignored.
;
; With striping, the database is spawned across multiple segments
; where each segment can have multiple stripes.
;
; Format of the lines below:
; Segment<number> = <size>, <stripe file name> [, <stripe file name> .. ]
;
; <number> must be ordered from 1 up.
;
; The <size> is the total size of the segment which is equally divided
; across all stripes forming the segment. Its specification can be in
; gigabytes (g), megabytes (m), kilobytes (k) or in database blocks
; (b, the default)
;
; Note that the segment size must be a multiple of the database page size
; which is currently 8k. Also, the segment size must be divisible by the
; number of stripe files forming the segment.
;
; The example below creates a 200 meg database striped on two segments
; with two stripes of 50 meg and one of 100 meg.
;
; You can always add more segments to the configuration, but once
; added, do not change the setup.
;
[Striping]
Segment1 = 100M, db-seg1-1.db, db-seg1-2.db
Segment2 = 100M, db-seg2-1.db
;...
;[TempStriping]
;Segment1 = 100M, db-seg1-1.db, db-seg1-2.db
;Segment2 = 100M, db-seg2-1.db
;...
;[Ucms]
;UcmPath = <path>
;Ucm1 = <file>
;Ucm2 = <file>
;...
[Zero Config]
;ServerName = virtuoso (LIN-072)
;ServerDSN = ZDSN
;SSLServerName =
;SSLServerDSN =
[Mono]
;MONO_TRACE = Off
;MONO_PATH = <path_here>
;MONO_ROOT = <path_here>
;MONO_CFG_DIR = <path_here>
;virtclr.dll =
[URIQA]
;DynamicLocal = 0
;DefaultHost = localhost:8890
[SPARQL]
;ExternalQuerySource = 1
;ExternalXsltSource = 1
;DefaultGraph = http://localhost:8890/dataspace
;ImmutableGraphs = http://localhost:8890/dataspace
ResultSetMaxRows = 80000000
MaxQueryCostEstimationTime = 360000 ; in seconds
MaxQueryExecutionTime = 360000 ; in seconds
DefaultQuery = select distinct ?Concept where {[] a
?Concept} LIMIT 100
DeferInferenceRulesInit = 0 ; controls inference rules loading
;PingService = http://rpc.pingthesemanticweb.com/
[Plugins]
;LoadPath = /scratch/virtuoso//lib/virtuoso/hosting
;Load1 = plain, wikiv
;Load2 = plain, mediawiki
;Load3 = plain, creolewiki
;Load4 = plain, im
;Load5 = plain, wbxml2
;Load6 = plain, hslookup
;Load7 = attach, libphp5.so
;Load8 = Hosting, hosting_php.so
;Load9 = Hosting,hosting_perl.so
;Load10 = Hosting,hosting_python.so
;Load11 = Hosting,hosting_ruby.so
;Load12 = msdtc,msdtc_sample
------------------------------------------------------------------------------
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