SPARQL query interrupts with memory errors

atima · March 28, 2021, 9:39pm

Hello there,

I am using Stardog 7.4.3 with the Stardog Studio IDE.
I had a simple SELECT SPARQL query on a 15K triple database which used to work perfectly.
After I used an INSERT DATA query and I have added some triples with the SPARQL, the database does NOT give me back any result for any SELECT query anymore.
The queries interrupt and the Stardog log file gives me the following result:

INFO 2021-03-28 22:47:58,661 [memory-monitor] com.complexible.stardog.api.NativeMemoryMonitor:reportStatus(135): System mem
Total Memory: 0
Available Memory: 0
INFO 2021-03-28 22:47:58,661 [memory-monitor] com.complexible.stardog.api.NativeMemoryMonitor:reportStatus(136): init = 2.0G used = 442M committed = 1.9G max = 1.9G
INFO 2021-03-28 22:47:58,661 [memory-monitor] com.complexible.stardog.api.NativeMemoryMonitor:reportStatus(137):
DETAILED MEMORY INFO
Heap Memory Usage: init = 2147483648(2097152K) used = 463223312(452366K) committed = 2058354688(2010112K) max = 2058354688(2010112K)
Non-Heap Memory Usage: init = 2555904(2496K) used = 74582120(72834K) committed = 78200832(76368K) max = -1(-1K)
Name: PS Scavenge
Collection count: 2
Collection time: 23
Memory Pools: [PS Eden Space, PS Survivor Space]
Name: PS MarkSweep
Collection count: 2
Collection time: 60
Memory Pools: [PS Eden Space, PS Survivor Space, PS Old Gen]

Memory Pools Info
Name: Code Cache
Usage: init = 2555904(2496K) used = 15645248(15278K) committed = 15990784(15616K) max = 251658240(245760K)
Collection Usage: null
Peak Usage: init = 2555904(2496K) used = 15854848(15483K) committed = 15990784(15616K) max = 251658240(245760K)
Type: Non-heap memory
Memory Manager Names: [CodeCacheManager]
Name: Metaspace
Usage: init = 0(0K) used = 51978752(50760K) committed = 54697984(53416K) max = -1(-1K)
Collection Usage: null
Peak Usage: init = 0(0K) used = 51978752(50760K) committed = 54697984(53416K) max = -1(-1K)
Type: Non-heap memory
Memory Manager Names: [Metaspace Manager]
Name: Compressed Class Space
Usage: init = 0(0K) used = 6958408(6795K) committed = 7512064(7336K) max = 1073741824(1048576K)
Collection Usage: null
Peak Usage: init = 0(0K) used = 6958408(6795K) committed = 7512064(7336K) max = 1073741824(1048576K)
Type: Non-heap memory
Memory Manager Names: [Metaspace Manager]
Name: PS Eden Space
Usage: init = 537395200(524800K) used = 441352408(431008K) committed = 537395200(524800K) max = 537395200(524800K)
Collection Usage: init = 537395200(524800K) used = 0(0K) committed = 537395200(524800K) max = 537395200(524800K)
Peak Usage: init = 537395200(524800K) used = 441352408(431008K) committed = 537395200(524800K) max = 537395200(524800K)
Type: Heap memory
Memory Manager Names: [PS MarkSweep, PS Scavenge]
Name: PS Survivor Space
Usage: init = 89128960(87040K) used = 0(0K) committed = 89128960(87040K) max = 89128960(87040K)
Collection Usage: init = 89128960(87040K) used = 0(0K) committed = 89128960(87040K) max = 89128960(87040K)
Peak Usage: init = 89128960(87040K) used = 20556320(20074K) committed = 89128960(87040K) max = 89128960(87040K)
Type: Heap memory
Memory Manager Names: [PS MarkSweep, PS Scavenge]
Name: PS Old Gen
Usage: init = 1431830528(1398272K) used = 21870904(21358K) committed = 1431830528(1398272K) max = 1431830528(1398272K)
Collection Usage: init = 1431830528(1398272K) used = 21870904(21358K) committed = 1431830528(1398272K) max = 1431830528(1398272K)
Peak Usage: init = 1431830528(1398272K) used = 21870904(21358K) committed = 1431830528(1398272K) max = 1431830528(1398272K)
Type: Heap memory
Memory Manager Names: [PS MarkSweep]

Would you please help me out with the problem?
I have read in some forums to set the STARDOG_JAVA_ARGS for the heap and direct memory. If this is the problem, could you tell me please how that must be done? Should I add the command to the stardog.properties file or to the stardog-admin.bat?

Many thanks in advance!

zachary.whitley · March 28, 2021, 11:03pm

You'd set that in an environment variable named STARDOG_JAVA_ARGS like the following

export STARDOG_JAVA_ARGS="-Xmx2g -Xms2g -XX:MaxDirectMemorySize=1g"

You'll need to restart stardog for it to be picked up. How exactly you set an env variable depends on your platform and how you installed it. Followup if you need any help with that.

atima · March 30, 2021, 5:32pm

Thank you so much for the quick response!
However, I have another silly question because I'm having difficulty setting the STARDOG_JAVA_ARGS.
I'm running Stardog on windows using the stardog-admin bat file, and I have tried to set the variable by a command line:
set STARDOG_JAVA_ARGS="-Xmx4g -Xms4g -XX:MaxDirectMemorySize=8g"

But then when I try to start the Stardog server with this command: "stardog-admin server start", it gives me this error: "-Xms4g was unexpected at this time".

Would you please help me to set the STARDOG_JAVA_ARGS on windows?

Another point is that I had no memory issue before running the INSERT DATA and my database is relatively small (15k triples) which should be ok with the default memory size.
I also tested this theory and made another database with the same triples, and again it had no issue running the queries at first, but after running the INSERT DATA query, the new database also came with memory errors. So basically the INSERT query runs successfully, but afterward, all other queries give this error.
I'd like to know what is the relation between them and if there's any specific way of inserting data without making this problem because I need to insert new triples in real time and be able to get the result.

Thank you so much for your time!

zachary.whitley · March 31, 2021, 1:11pm

Not a silly question. I'm not a Windows person but I believe the problem with the STARDOG_JAVA_ARGS is caused by the first space and the way you need to quote things when using set. Try running `set "STARDOG_JAVA_ARGS=-Xmx4g -Xms4g -XX:MaxDirectMemorySize=8g"

The memory thing does seem odd and that definitely shouldn't be happening. Can you take a look at your stardog.log file and see if there are any warnings or errors and include them here?

atima · March 31, 2021, 3:37pm

Thanks a bunch!
The issue with STARDOG_JAVA_ARGS is solved and I have more memory allocated now.
However, I still receive the same error in the log file:

INFO 2021-03-31 17:17:22,374 [main] com.complexible.stardog.StardogLicense:main(405): Checking for valid license...
INFO 2021-03-31 17:17:25,961 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(466): Initializing virtual graph registry
INFO 2021-03-31 17:17:26,002 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(490): Loaded virtual graph registry with 0 entries
INFO 2021-03-31 17:17:28,208 [memory-monitor] com.complexible.stardog.api.NativeMemoryMonitor:reportStatus(127): Memory usage NaN% - initiating detailed analysis - will check again in 1m
INFO 2021-03-31 17:17:28,209 [memory-monitor] com.complexible.stardog.api.NativeMemoryMonitor:reportStatus(128): Stardog JVM memory usage
OSMemory{ virtualSize=0B, residentSize=0B, residentSizePeak=0B, regionCount=0, pinnedSize=0B, vmTotal=0B, vmAvailable=0B, pageSize=0B}
INFO 2021-03-31 17:17:28,217 [memory-monitor] com.complexible.stardog.api.NativeMemoryMonitor:reportStatus(133): Stardog Metrics
dbms.memory.blockcache.data.add.count = 77
dbms.memory.blockcache.data.add.failure.count = 0
dbms.memory.blockcache.data.cachesIndexBlocks = false
dbms.memory.blockcache.data.capacity = 1,142,461,184
dbms.memory.blockcache.data.hits = 169
dbms.memory.blockcache.data.iteratorCreated = 0
dbms.memory.blockcache.data.iteratorDeleted = 0
dbms.memory.blockcache.data.misses = 77
dbms.memory.blockcache.data.pinnedUsage = 0
dbms.memory.blockcache.data.ratio = 0.6869918699186992
dbms.memory.blockcache.data.read = 3,176,001
dbms.memory.blockcache.data.strictCapacity = true
dbms.memory.blockcache.data.usage = 540,028
dbms.memory.blockcache.data.written = 4,581,067
dbms.memory.blockcache.dictionary.add.count = 70
dbms.memory.blockcache.dictionary.add.failure.count = 0
dbms.memory.blockcache.dictionary.cachesIndexBlocks = true
dbms.memory.blockcache.dictionary.capacity = 571,230,592
dbms.memory.blockcache.dictionary.hits = 1,201
dbms.memory.blockcache.dictionary.iteratorCreated = 0
dbms.memory.blockcache.dictionary.iteratorDeleted = 0
dbms.memory.blockcache.dictionary.misses = 70
dbms.memory.blockcache.dictionary.pinnedUsage = 0
dbms.memory.blockcache.dictionary.ratio = 0.94492525570417
dbms.memory.blockcache.dictionary.read = 4,980,731
dbms.memory.blockcache.dictionary.strictCapacity = true
dbms.memory.blockcache.dictionary.usage = 104,298
dbms.memory.blockcache.dictionary.written = 241,087
dbms.memory.blockcache.total.capacity = 1,999,307,072
dbms.memory.blockcache.total.data.hits = 0
dbms.memory.blockcache.total.data.misses = 0
dbms.memory.blockcache.total.data.ratio = 0.0
dbms.memory.blockcache.total.filter.hits = 0
dbms.memory.blockcache.total.filter.misses = 0
dbms.memory.blockcache.total.filter.ratio = 0.0
dbms.memory.blockcache.total.index.hits = 0
dbms.memory.blockcache.total.index.misses = 0
dbms.memory.blockcache.total.index.ratio = 0.0
dbms.memory.blockcache.total.iteratorCreated = 0
dbms.memory.blockcache.total.iteratorDeleted = 0
dbms.memory.blockcache.total.pinnedUsage = 0
dbms.memory.blockcache.total.usage = 672,567
dbms.memory.blockcache.txn.add.count = 124
dbms.memory.blockcache.txn.add.failure.count = 0
dbms.memory.blockcache.txn.cachesIndexBlocks = true
dbms.memory.blockcache.txn.capacity = 285,615,296
dbms.memory.blockcache.txn.hits = 3,246
dbms.memory.blockcache.txn.iteratorCreated = 0
dbms.memory.blockcache.txn.iteratorDeleted = 0
dbms.memory.blockcache.txn.misses = 124
dbms.memory.blockcache.txn.pinnedUsage = 0
dbms.memory.blockcache.txn.ratio = 0.9632047477744807
dbms.memory.blockcache.txn.read = 997,864
dbms.memory.blockcache.txn.strictCapacity = true
dbms.memory.blockcache.txn.usage = 28,241
dbms.memory.blockcache.txn.written = 28,416
dbms.memory.config.dict_index_cache = 823,237,018
dbms.memory.config.dict_value_cache = 823,237,018
dbms.memory.config.query_mem_blocks = 2,448,131,358
dbms.memory.config.starrocks_size = 5,712,306,504
dbms.memory.direct.buffer.used = 8,248
dbms.memory.heap.max = 4,116,185,088
dbms.memory.heap.query.blocks.max = 0
dbms.memory.heap.query.blocks.used = 0
dbms.memory.heap.used = 240,173,552
dbms.memory.management = NATIVE
dbms.memory.mapped.used = 0
dbms.memory.mode = DEFAULT{Starrocks.block_cache=20, Starrocks.dict_block_cache=10, Native.starrocks=70, Heap.dict_value=50, Starrocks.txn_block_cache=5, Heap.dict_index=50, Starrocks.memtable=40, Starrocks.untracked_memory=20, Starrocks.buffer_pool=5, Native.query=30}
dbms.memory.monitor.interval = 60000
dbms.memory.monitor.report.threshold = 0.9
dbms.memory.native.max = 8,589,934,592
dbms.memory.native.query.blocks.max = 2,448,131,358
dbms.memory.native.query.blocks.used = 0
dbms.memory.system.pageSize = 0
dbms.memory.system.pinnedSize = 0
dbms.memory.system.regionCount = 0
dbms.memory.system.rss = 0
dbms.memory.system.rss.peak = 0
dbms.memory.system.usageRatio = NaN
dbms.memory.system.virtual = 0
INFO 2021-03-31 17:17:28,218 [memory-monitor] com.complexible.stardog.api.NativeMemoryMonitor:reportStatus(135): System mem
Total Memory: 0
Available Memory: 0
INFO 2021-03-31 17:17:28,218 [memory-monitor] com.complexible.stardog.api.NativeMemoryMonitor:reportStatus(136): init = 4.0G used = 229M committed = 3.8G max = 3.8G
INFO 2021-03-31 17:17:28,220 [memory-monitor] com.complexible.stardog.api.NativeMemoryMonitor:reportStatus(137):
DETAILED MEMORY INFO
Heap Memory Usage: init = 4294967296(4194304K) used = 240173552(234544K) committed = 4116185088(4019712K) max = 4116185088(4019712K)
Non-Heap Memory Usage: init = 2555904(2496K) used = 63488424(62000K) committed = 66076672(64528K) max = -1(-1K)
Name: PS Scavenge
Collection count: 2
Collection time: 24
Memory Pools: [PS Eden Space, PS Survivor Space]
Name: PS MarkSweep
Collection count: 2
Collection time: 60
Memory Pools: [PS Eden Space, PS Survivor Space, PS Old Gen]

Memory Pools Info
Name: Code Cache
Usage: init = 2555904(2496K) used = 13979072(13651K) committed = 14090240(13760K) max = 251658240(245760K)
Collection Usage: null
Peak Usage: init = 2555904(2496K) used = 13988928(13661K) committed = 14090240(13760K) max = 251658240(245760K)
Type: Non-heap memory
Memory Manager Names: [CodeCacheManager]
Name: Metaspace
Usage: init = 0(0K) used = 43658016(42634K) committed = 45654016(44584K) max = -1(-1K)
Collection Usage: null
Peak Usage: init = 0(0K) used = 43658512(42635K) committed = 45654016(44584K) max = -1(-1K)
Type: Non-heap memory
Memory Manager Names: [Metaspace Manager]
Name: Compressed Class Space
Usage: init = 0(0K) used = 5862648(5725K) committed = 6332416(6184K) max = 1073741824(1048576K)
Collection Usage: null
Peak Usage: init = 0(0K) used = 5862648(5725K) committed = 6332416(6184K) max = 1073741824(1048576K)
Type: Non-heap memory
Memory Manager Names: [Metaspace Manager]
Name: PS Eden Space
Usage: init = 1073741824(1048576K) used = 218361176(213243K) committed = 1073741824(1048576K) max = 1073741824(1048576K)
Collection Usage: init = 1073741824(1048576K) used = 0(0K) committed = 1073741824(1048576K) max = 1073741824(1048576K)
Peak Usage: init = 1073741824(1048576K) used = 300655936(293609K) committed = 1073741824(1048576K) max = 1073741824(1048576K)
Type: Heap memory
Memory Manager Names: [PS MarkSweep, PS Scavenge]
Name: PS Survivor Space
Usage: init = 178782208(174592K) used = 0(0K) committed = 178782208(174592K) max = 178782208(174592K)
Collection Usage: init = 178782208(174592K) used = 0(0K) committed = 178782208(174592K) max = 178782208(174592K)
Peak Usage: init = 178782208(174592K) used = 20647512(20163K) committed = 178782208(174592K) max = 178782208(174592K)
Type: Heap memory
Memory Manager Names: [PS MarkSweep, PS Scavenge]
Name: PS Old Gen
Usage: init = 2863661056(2796544K) used = 21812376(21301K) committed = 2863661056(2796544K) max = 2863661056(2796544K)
Collection Usage: init = 2863661056(2796544K) used = 21812376(21301K) committed = 2863661056(2796544K) max = 2863661056(2796544K)
Peak Usage: init = 2863661056(2796544K) used = 21812376(21301K) committed = 2863661056(2796544K) max = 2863661056(2796544K)
Type: Heap memory
Memory Manager Names: [PS MarkSweep]

INFO 2021-03-31 17:17:28,224 [main] com.complexible.stardog.StardogKernel:start(2296): Initializing Stardog
INFO 2021-03-31 17:17:28,637 [main] com.complexible.stardog.search.db.ConnectableSearchIndex:initialize(141): The search.index.vacuum option is off so stale literals are left in the search index for test
INFO 2021-03-31 17:17:29,244 [main] com.complexible.stardog.cli.impl.ServerStart:call(256): Memory options
INFO 2021-03-31 17:17:29,245 [main] com.complexible.stardog.cli.impl.ServerStart:call(257): Memory mode: DEFAULT{Starrocks.block_cache=20, Starrocks.dict_block_cache=10, Native.starrocks=70, Heap.dict_value=50, Starrocks.txn_block_cache=5, Heap.dict_index=50, Starrocks.memtable=40, Starrocks.untracked_memory=20, Starrocks.buffer_pool=5, Native.query=30}
INFO 2021-03-31 17:17:29,245 [main] com.complexible.stardog.cli.impl.ServerStart:call(258): Min Heap Size: 4.0G
INFO 2021-03-31 17:17:29,245 [main] com.complexible.stardog.cli.impl.ServerStart:call(259): Max Heap Size: 3.8G
INFO 2021-03-31 17:17:29,245 [main] com.complexible.stardog.cli.impl.ServerStart:call(260): Max Direct Mem: 8.0G
INFO 2021-03-31 17:17:29,246 [main] com.complexible.stardog.cli.impl.ServerStart:call(261): System Memory: 16G
ERROR 2021-03-31 17:17:54,003 [stardog-user-5] com.complexible.stardog.QueryManager:exceptionTriggered(473): Error during execution of the query
against database March with reasoning schema default
com.clarkparsia.pellet.api.exceptions.InconsistentOntologyException: null
at com.clarkparsia.pellet.api.query.impl.DefaultQueryEngine.execute(DefaultQueryEngine.java:89) ~[stardog-reasoning-shared-7.4.3.jar:?]
at com.clarkparsia.pellet.api.query.impl.AbstractQueryEngine.visit(AbstractQueryEngine.java:104) ~[stardog-reasoning-shared-7.4.3.jar:?]
at com.clarkparsia.pellet.api.query.impl.AbstractQueryEngine.visit(AbstractQueryEngine.java:33) ~[stardog-reasoning-shared-7.4.3.jar:?]
at com.clarkparsia.pellet.api.query.impl.SelectQueryImpl.accept(SelectQueryImpl.java:43) ~[stardog-reasoning-shared-7.4.3.jar:?]
at com.clarkparsia.pellet.api.query.impl.AbstractQueryEngine.execute(AbstractQueryEngine.java:42) ~[stardog-reasoning-shared-7.4.3.jar:?]
at com.complexible.stardog.reasoning.pellet.PelletUtils.executeQuery(PelletUtils.java:89) ~[stardog-reasoning-core-7.4.3.jar:?]
at com.complexible.stardog.reasoning.pellet.PelletOp.computeNext(PelletOp.java:89) ~[stardog-reasoning-core-7.4.3.jar:?]
at com.complexible.stardog.reasoning.pellet.PelletOp.computeNext(PelletOp.java:35) ~[stardog-reasoning-core-7.4.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:147) ~[stardog-utils-common-7.4.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:134) ~[stardog-utils-common-7.4.3.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.SingleProjectionOp.computeNext(SingleProjectionOp.java:88) ~[stardog-7.4.3.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.SingleProjectionOp.computeNext(SingleProjectionOp.java:29) ~[stardog-7.4.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:147) ~[stardog-utils-common-7.4.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:134) ~[stardog-utils-common-7.4.3.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.SliceOp._hasNext(SliceOp.java:92) ~[stardog-7.4.3.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.SliceOp.computeNext(SliceOp.java:100) ~[stardog-7.4.3.jar:?]
at com.complexible.stardog.plan.eval.operator.impl.SliceOp.computeNext(SliceOp.java:26) ~[stardog-7.4.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:147) ~[stardog-utils-common-7.4.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:134) ~[stardog-utils-common-7.4.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:149) ~[stardog-7.4.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:28) ~[stardog-7.4.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:147) ~[stardog-utils-common-7.4.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:134) ~[stardog-utils-common-7.4.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.OpBasedBindingSetIteration.computeNext(OpBasedBindingSetIteration.java:119) ~[stardog-7.4.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.OpBasedBindingSetIteration.computeNext(OpBasedBindingSetIteration.java:40) ~[stardog-7.4.3.jar:?]
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:141) ~[guava-27.0-jre.jar:?]
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:136) ~[guava-27.0-jre.jar:?]
at com.complexible.common.base.CloseableIterator$2.computeNext(CloseableIterator.java:84) ~[stardog-utils-common-7.4.3.jar:?]
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:141) ~[guava-27.0-jre.jar:?]
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:136) ~[guava-27.0-jre.jar:?]
at com.complexible.common.rdf.query.IteratorAsTupleQueryResult.computeNext(IteratorAsTupleQueryResult.java:81) ~[stardog-utils-rdf-7.4.3.jar:?]
at com.complexible.common.rdf.query.IteratorAsTupleQueryResult.computeNext(IteratorAsTupleQueryResult.java:23) ~[stardog-utils-rdf-7.4.3.jar:?]
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:141) ~[guava-27.0-jre.jar:?]
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:136) ~[guava-27.0-jre.jar:?]
at com.stardog.stark.query.ClosingSpliterator.forEachRemaining(ClosingSpliterator.java:37) ~[stardog-stark-query-api-7.4.3.jar:?]
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580) ~[?:1.8.0_191]
at com.stardog.stark.query.io.QueryResultWriters.write(QueryResultWriters.java:142) ~[stardog-stark-query-io-7.4.3.jar:?]
at com.stardog.stark.query.io.QueryResultWriters.write(QueryResultWriters.java:127) ~[stardog-stark-query-io-7.4.3.jar:?]
at com.complexible.stardog.protocols.http.server.ProtocolUtils.writeTupleResponse(ProtocolUtils.java:696) ~[stardog-protocols-http-server-7.4.3.jar:?]
at com.complexible.stardog.protocols.http.server.ProtocolUtils.executeReadQuery(ProtocolUtils.java:588) ~[stardog-protocols-http-server-7.4.3.jar:?]
at com.complexible.stardog.protocols.http.server.ProtocolUtils.executeReadQuery(ProtocolUtils.java:560) ~[stardog-protocols-http-server-7.4.3.jar:?]
at com.complexible.stardog.protocols.http.server.ProtocolUtils.executeReadQuery(ProtocolUtils.java:521) ~[stardog-protocols-http-server-7.4.3.jar:?]
at com.complexible.stardog.protocols.http.server.SPARQLProtocol.executeQuery(SPARQLProtocol.java:147) ~[stardog-protocols-http-server-7.4.3.jar:?]
at com.complexible.stardog.protocols.http.server.SPARQLProtocol.post(SPARQLProtocol.java:107) ~[stardog-protocols-http-server-7.4.3.jar:?]
at com.stardog.http.server.undertow.jaxrs.ExtractRoutes.lambda$handleIt$5(ExtractRoutes.java:192) ~[stardog-protocols-http-server-7.4.3.jar:?]
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) [shiro-core-1.6.0.jar:1.6.0]
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) [shiro-core-1.6.0.jar:1.6.0]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_191]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_191]
at java.lang.Thread.run(Thread.java:748) [?:1.8.0_191]

So basically I create a database, I run any Select query and everything is fine, then I run an INSERT data query successfully with no error, and after that, I run another SELECT query and it gives me this error and I'm no longer able to run any other queries.

Any help is highly appreciated!

stephen · April 1, 2021, 2:54pm

Hi,

Can you try setting the STARDOG_SERVER_JAVA_ARGS environment variable as well? This one specifically governs the server start command and therefore the running server that you're starting up.

If that still doesn't work, it looks like something could be amiss with the native memory monitor.

atima · April 2, 2021, 5:08pm

Thank you Stephen!
I set the STARDOG_SERVER_JAVA_ARGS as you suggested but it still gives me the same error.
Is there any way to solve this issue you mentioned about the native memory monitor?

I was also suspicious if this can have anything to do with my 1-year academic license? Is there any limitation to this license in inserting data?
Or is there any particular way for inserting data queries to avoid this problem?

Many thanks in advance...

atima · April 7, 2021, 1:14pm

Hello,
Is there any update on this issue? Because I am still struggling and can't find the reason.
Whenever I run the INSERT DATA query, I cannot run any other query after that, and basically my database becomes useless.
Any help is highly appreciated.
Thanks!

zachary.whitley · April 7, 2021, 2:36pm

Did you enable DL reasoning? It appears as though you've selected DL reasoning and your ontology is inconsistent. You may want to take a look at the reasoning consistency command and the icv.consistency.automatic configuration setting.

system · April 21, 2021, 2:37pm

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