Merge branch 'master' of https://github.com/arvados/bh20-seq-resource

1 files changed, 250 insertions, 0 deletions

diff --git a/etc/virtuoso-ose/virtuoso.ini b/etc/virtuoso-ose/virtuoso.ini
new file mode 100644
index 0000000..5da19ec
--- /dev/null
+++ b/etc/virtuoso-ose/virtuoso.ini
@@ -0,0 +1,250 @@
+;
+;  virtuoso.ini
+;
+;  Configuration file for the OpenLink Virtuoso VDBMS Server
+;
+;  Make sure to change the dba:dba password!
+;
+;  To learn more about this product, or any other product in our
+;  portfolio, please check out our web site at:
+;
+;      http://virtuoso.openlinksw.com/
+;
+;  Database setup
+;
+[Database]
+DatabaseFile			= /export/virtuoso/var/lib/virtuoso/db/virtuoso.db
+ErrorLogFile			= /export/virtuoso/var/lib/virtuoso/db/virtuoso.log
+LockFile			= /export/virtuoso/var/lib/virtuoso/db/virtuoso.lck
+TransactionFile			= /export/virtuoso/var/lib/virtuoso/db/virtuoso.trx
+xa_persistent_file		= /export/virtuoso/var/lib/virtuoso/db/virtuoso.pxa
+ErrorLogLevel			= 7
+FileExtend			= 200
+MaxCheckpointRemap		= 2000
+Striping			= 0
+TempStorage			= TempDatabase
+
+
+[TempDatabase]
+DatabaseFile			= /export/virtuoso/var/lib/virtuoso/db/virtuoso-temp.db
+TransactionFile			= /export/virtuoso/var/lib/virtuoso/db/virtuoso-temp.trx
+MaxCheckpointRemap		= 2000
+Striping			= 0
+
+;
+;  Server parameters
+;
+[Parameters]
+ServerPort			= 1111
+LiteMode			= 0
+DisableUnixSocket		= 1
+DisableTcpSocket		= 0
+;SSLServerPort			= 2111
+;SSLCertificate			= cert.pem
+;SSLPrivateKey			= pk.pem
+;X509ClientVerify		= 0
+;X509ClientVerifyDepth		= 0
+;X509ClientVerifyCAFile		= ca.pem
+MaxClientConnections		= 10
+CheckpointInterval		= 60
+O_DIRECT			= 0
+CaseMode			= 2
+MaxStaticCursorRows		= 5000
+CheckpointAuditTrail		= 0
+AllowOSCalls			= 0
+SchedulerInterval		= 10
+DirsAllowed			= ., ~/opt/virtuoso/share/virtuoso/vad
+ThreadCleanupInterval		= 0
+ThreadThreshold			= 10
+ResourcesCleanupInterval	= 0
+FreeTextBatchSize		= 100000
+SingleCPU			= 0
+VADInstallDir			= ~/opt/virtuoso/share/virtuoso/vad
+PrefixResultNames               = 0
+RdfFreeTextRulesSize		= 100
+IndexTreeMaps			= 256
+MaxMemPoolSize                  = 200000000
+PrefixResultNames               = 0
+MacSpotlight                    = 0
+IndexTreeMaps                   = 64
+MaxQueryMem 		 	= 2G		; memory allocated to query processor
+VectorSize 		 	= 1000		; initial parallel query vector (array of query operations) size
+MaxVectorSize 		 	= 1000000	; query vector size threshold.
+AdjustVectorSize 	 	= 0
+ThreadsPerQuery 	 	= 4
+AsyncQueueMaxThreads 	 	= 10
+;;
+;; 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
+
+
+[HTTPServer]
+ServerPort			= 8890
+ServerRoot			= /export/virtuoso/var/lib/virtuoso/vsp
+MaxClientConnections		= 10
+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
+MaintenancePage             	= atomic.html
+EnabledGzipContent          	= 1
+
+
+[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-localhost
+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 (localhost)
+;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           	= 10000
+MaxQueryCostEstimationTime 	= 400	; in seconds
+MaxQueryExecutionTime      	= 60	; in seconds
+DefaultQuery               	= select distinct ?Concept where {[] a ?Concept} LIMIT 100
+DeferInferenceRulesInit    	= 0  ; controls inference rules loading
+;PingService       		= http://rpc.pingthesemanticweb.com/
+
+
+[Plugins]
+; LoadPath			= /home/wrk/opt/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