# Memory error after server upgrade

**URL:** https://community.stardog.com/t/memory-error-after-server-upgrade/1259
**Category:** Bug
**Created:** [August 27, 2018, 6:47pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259 "2018-08-27T18:47:27Z")
**Posts on this page:** 10
**Page:** 1

<div class="post-metadata">

### Author: ![semanticfire](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/semanticfire/32/47_2.png) [@semanticfire](https://community.stardog.com/u/semanticfire)
#### Post date: [August 27, 2018, 6:47pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/1 "2018-08-27T18:47:27Z")

</div>

Hi after upgrading to 5.3.3 on a server I run into the following error, the system does seem to function as expected though

```
Computing statistics: 51% complete in 00:01:11 (183,1K triples/sec)
ERROR 2018-08-27 20:42:57,052 [main] com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder:build(121): Error computing the selectivity statistics
com.complexible.stardog.index.IndexException: java.lang.OutOfMemoryError: GC overhead limit exceeded
	at com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder.build(ConcurrentCharacteristicSetStatisticsBuilder.java:93) ~[stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.statistics.DiskCharacteristicSetsStatisticsBuilder.build(DiskCharacteristicSetsStatisticsBuilder.java:114) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.statistics.DiskCharacteristicSetsStatisticsLoader.rebuild(DiskCharacteristicSetsStatisticsLoader.java:107) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.statistics.DiskCharacteristicSetsStatisticsLoader.load(DiskCharacteristicSetsStatisticsLoader.java:64) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.DiskIndex.<init>(DiskIndex.java:43) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.DefaultDiskIndexReader.read(DefaultDiskIndexReader.java:129) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.io.IndexIO.read(IndexIO.java:324) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.db.DatabaseFactoryImpl.read(DatabaseFactoryImpl.java:126) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.db.DatabaseFactoryImpl.read(DatabaseFactoryImpl.java:55) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.StardogKernel.openDatabase(StardogKernel.java:2708) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.StardogKernel.initDatabases(StardogKernel.java:2432) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.StardogKernel.start(StardogKernel.java:2335) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.StardogKernel.initialize(StardogKernel.java:799) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.Stardog.initKernel(Stardog.java:214) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.Stardog.<init>(Stardog.java:206) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.Stardog.<init>(Stardog.java:60) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.Stardog$StardogBuilder.create(Stardog.java:597) [stardog-5.3.3.jar:?]
	at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:162) [stardog-cli-5.3.3.jar:?]
	at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:41) [stardog-cli-5.3.3.jar:?]
	at com.complexible.stardog.cli.CLIBase.execute(CLIBase.java:55) [stardog-cli-5.3.3.jar:?]
	at com.complexible.stardog.cli.admin.CLI.main(CLI.java:186) [stardog-cli-5.3.3.jar:?]
Caused by: java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: GC overhead limit exceeded
	at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:1.8.0_181]
	at java.util.concurrent.FutureTask.get(FutureTask.java:192) ~[?:1.8.0_181]
	at com.complexible.common.util.concurrent.ExecutionGroup$1.executeAndWait(ExecutionGroup.java:78) ~[stardog-utils-common-5.3.3.jar:?]
	at com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder.build(ConcurrentCharacteristicSetStatisticsBuilder.java:88) ~[stardog-5.3.3.jar:?]
	... 20 more
	Suppressed: java.util.concurrent.ExecutionException: com.complexible.stardog.index.IndexException: java.lang.OutOfMemoryError: GC overhead limit exceeded
		at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:1.8.0_181]
		at java.util.concurrent.FutureTask.get(FutureTask.java:192) ~[?:1.8.0_181]
		at com.complexible.common.util.concurrent.ExecutionGroup$1.executeAndWait(ExecutionGroup.java:78) ~[stardog-utils-common-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder.build(ConcurrentCharacteristicSetStatisticsBuilder.java:88) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.disk.statistics.DiskCharacteristicSetsStatisticsBuilder.build(DiskCharacteristicSetsStatisticsBuilder.java:114) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.disk.statistics.DiskCharacteristicSetsStatisticsLoader.rebuild(DiskCharacteristicSetsStatisticsLoader.java:107) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.disk.statistics.DiskCharacteristicSetsStatisticsLoader.load(DiskCharacteristicSetsStatisticsLoader.java:64) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.disk.DiskIndex.<init>(DiskIndex.java:43) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.disk.DefaultDiskIndexReader.read(DefaultDiskIndexReader.java:129) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.io.IndexIO.read(IndexIO.java:324) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.db.DatabaseFactoryImpl.read(DatabaseFactoryImpl.java:126) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.db.DatabaseFactoryImpl.read(DatabaseFactoryImpl.java:55) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.StardogKernel.openDatabase(StardogKernel.java:2708) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.StardogKernel.initDatabases(StardogKernel.java:2432) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.StardogKernel.start(StardogKernel.java:2335) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.StardogKernel.initialize(StardogKernel.java:799) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.Stardog.initKernel(Stardog.java:214) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.Stardog.<init>(Stardog.java:206) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.Stardog.<init>(Stardog.java:60) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.Stardog$StardogBuilder.create(Stardog.java:597) [stardog-5.3.3.jar:?]
		at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:162) [stardog-cli-5.3.3.jar:?]
		at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:41) [stardog-cli-5.3.3.jar:?]
		at com.complexible.stardog.cli.CLIBase.execute(CLIBase.java:55) [stardog-cli-5.3.3.jar:?]
		at com.complexible.stardog.cli.admin.CLI.main(CLI.java:186) [stardog-cli-5.3.3.jar:?]
	Caused by: com.complexible.stardog.index.IndexException: java.lang.OutOfMemoryError: GC overhead limit exceeded
		at com.complexible.stardog.index.statistics.ComputePropertyStatistics.compute(ComputePropertyStatistics.java:44) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder.computePropertyStatistics(ConcurrentCharacteristicSetStatisticsBuilder.java:49) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder.lambda$build$1(ConcurrentCharacteristicSetStatisticsBuilder.java:85) ~[stardog-5.3.3.jar:?]
		at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[?:1.8.0_181]
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) ~[?:1.8.0_181]
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ~[?:1.8.0_181]
		at java.lang.Thread.run(Thread.java:748) ~[?:1.8.0_181]
	Caused by: java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: GC overhead limit exceeded
		at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:1.8.0_181]
		at java.util.concurrent.FutureTask.get(FutureTask.java:192) ~[?:1.8.0_181]
		at com.complexible.common.util.concurrent.ExecutionGroup$1.executeAndWait(ExecutionGroup.java:78) ~[stardog-utils-common-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ComputePropertyStatistics.compute(ComputePropertyStatistics.java:41) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder.computePropertyStatistics(ConcurrentCharacteristicSetStatisticsBuilder.java:49) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder.lambda$build$1(ConcurrentCharacteristicSetStatisticsBuilder.java:85) ~[stardog-5.3.3.jar:?]
		at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[?:1.8.0_181]
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) ~[?:1.8.0_181]
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ~[?:1.8.0_181]
		at java.lang.Thread.run(Thread.java:748) ~[?:1.8.0_181]
	Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
		at com.complexible.stardog.index.BinaryCounts.create(BinaryCounts.java:89) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.disk.compression.BinaryTransformers$2.create(BinaryTransformers.java:78) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.IndexOrders.lambda$null$1(IndexOrders.java:79) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.IndexOrders$$Lambda$243/1799535763.apply(Unknown Source) ~[?:?]
		at com.complexible.stardog.index.StreamingCountingIndexIterator.computeNext(StreamingCountingIndexIterator.java:67) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.StreamingCountingIndexIterator.computeNext(StreamingCountingIndexIterator.java:17) ~[stardog-5.3.3.jar:?]
		at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-5.3.3.jar:?]
		at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ComputePropertyStatistics.computeDegrees(ComputePropertyStatistics.java:99) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ComputePropertyStatistics.computeDomains(ComputePropertyStatistics.java:71) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ComputePropertyStatistics.lambda$compute$0(ComputePropertyStatistics.java:38) ~[stardog-5.3.3.jar:?]
		at com.complexible.stardog.index.statistics.ComputePropertyStatistics$$Lambda$238/56711263.call(Unknown Source) ~[?:?]
		at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[?:1.8.0_181]
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) ~[?:1.8.0_181]
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ~[?:1.8.0_181]
		at java.lang.Thread.run(Thread.java:748) ~[?:1.8.0_181]
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
	at com.complexible.common.trie.Trie$Node.<init>(Trie.java:366) ~[stardog-utils-common-5.3.3.jar:?]
	at com.complexible.common.trie.Trie$Node.addChild(Trie.java:371) ~[stardog-utils-common-5.3.3.jar:?]
	at com.complexible.common.trie.Trie.put(Trie.java:57) ~[stardog-utils-common-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.DiskTrie.put(DiskTrie.java:94) ~[stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.btree.impl.BPlusTreeBackedTrie.lambda$addAll$0(BPlusTreeBackedTrie.java:44) ~[stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.btree.impl.BPlusTreeBackedTrie$$Lambda$267/2127412082.accept(Unknown Source) ~[?:?]
	at java.util.Iterator.forEachRemaining(Iterator.java:116) ~[?:1.8.0_181]
	at com.complexible.stardog.index.disk.btree.impl.BPlusTreeBackedTrie.addAll(BPlusTreeBackedTrie.java:44) ~[stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.statistics.DiskCharacteristicSets.addAll(DiskCharacteristicSets.java:49) ~[stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.statistics.DiskCharacteristicSetsStatisticsBuilder.computeCharacteristicSets(DiskCharacteristicSetsStatisticsBuilder.java:85) ~[stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.disk.statistics.DiskCharacteristicSetsStatisticsBuilder.computeCharacteristicSets(DiskCharacteristicSetsStatisticsBuilder.java:36) ~[stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder.lambda$build$0(ConcurrentCharacteristicSetStatisticsBuilder.java:82) ~[stardog-5.3.3.jar:?]
	at com.complexible.stardog.index.statistics.ConcurrentCharacteristicSetStatisticsBuilder$$Lambda$235/1389426051.call(Unknown Source) ~[?:?]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[?:1.8.0_181]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) ~[?:1.8.0_181]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ~[?:1.8.0_181]
	at java.lang.Thread.run(Thread.java:748) ~[?:1.8.0_181]
```

---

<div class="post-metadata">

### Author: ![pavel](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/pavel/32/18_2.png) [@pavel](https://community.stardog.com/u/pavel)
#### Post date: [August 27, 2018, 7:00pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/2 "2018-08-27T19:00:31Z")

</div>

This indicates that selectivity statistics wasn’t computed for one or more databases due to insufficient amount of heap. This may result in slower queries. Ideally you’d bump the memory (`$STARDOG_SERVER_JAVA_ARGS`) and restart the server. In theory you can also manually run `stardog-admin db optimize <db name>` on your database (or all of them).

Cheers,  
Pavel

---

<div class="post-metadata">

### Author: ![semanticfire](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/semanticfire/32/47_2.png) [@semanticfire](https://community.stardog.com/u/semanticfire)
#### Post date: [August 27, 2018, 7:04pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/3 "2018-08-27T19:04:54Z")

</div>

What if my JAVA\_ARGS are maxed out to the physical available memory ?

---

<div class="post-metadata">

### Author: ![pavel](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/pavel/32/18_2.png) [@pavel](https://community.stardog.com/u/pavel)
#### Post date: [August 27, 2018, 7:11pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/4 "2018-08-27T19:11:53Z")

</div>

How large are your databases and what’s in `$STARDOG_SERVER_JAVA_ARGS`?

---

<div class="post-metadata">

### Author: ![semanticfire](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/semanticfire/32/47_2.png) [@semanticfire](https://community.stardog.com/u/semanticfire)
#### Post date: [August 27, 2018, 7:13pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/5 "2018-08-27T19:13:41Z")

</div>

I’ve got about 33G on disk data, system memory is 4G

---

<div class="post-metadata">

### Author: ![pavel](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/pavel/32/18_2.png) [@pavel](https://community.stardog.com/u/pavel)
#### Post date: [August 27, 2018, 7:31pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/6 "2018-08-27T19:31:03Z")

</div>

Do you mean 33G of data in one database or all of them? If that's one database, my guess would be it's over 100M triples and then your server has considerably less memory than suggested in [1] (which also tends to be on the lower side). What does `stardog-admin db status` print?

[1] [Home | Stardog Documentation Latest](https://www.stardog.com/docs/#_capacity_planning)

---

<div class="post-metadata">

### Author: ![semanticfire](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/semanticfire/32/47_2.png) [@semanticfire](https://community.stardog.com/u/semanticfire)
#### Post date: [August 27, 2018, 7:39pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/7 "2018-08-27T19:39:24Z")

</div>

I’m talking about all the databases, some of them are not really active, but can be relatively large ( although below 100M )

You need to work on a command to get this info for all databases 🙂

---

<div class="post-metadata">

### Author: ![pavel](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/pavel/32/18_2.png) [@pavel](https://community.stardog.com/u/pavel)
#### Post date: [August 27, 2018, 8:00pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/8 "2018-08-27T20:00:40Z")

</div>

If large databases are not used but your server has only 4G, then it’s reasonable to take them out (e.g. back up and then remove). They still use some resources even if not really used. Normally it’s not a big deal but in your situation it might help.

Cheers,  
Pavel

---

<div class="post-metadata">

### Author: ![evren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/evren/32/1515_2.png) [@evren](https://community.stardog.com/u/evren)
#### Post date: [August 28, 2018, 5:57am UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/9 "2018-08-28T05:57:35Z")

</div>

Bart,

You can use the `stardog-admin server status` command which will print the size of each database along with other statistics.

Best,  
Evren

---

<div class="post-metadata">

### Author: ![semanticfire](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.stardog.com/semanticfire/32/47_2.png) [@semanticfire](https://community.stardog.com/u/semanticfire)
#### Post date: [August 30, 2018, 12:37pm UTC](https://community.stardog.com/t/memory-error-after-server-upgrade/1259/10 "2018-08-30T12:37:09Z")

</div>

When I try to do the optimize per database the command line states 'succesfully optimezed ’ but the server console signals a GC error.

A new server restart results in the same error as before.