Yeah. Thanks! my problem is solved by using that setConfig and removing the 
registerShutDownHook();

Another option I have is deleting all nodes/relationships and then add new 
ones to that. However, until some days ago, I didn't even know the problem 
is for creating multiple instances (I thought with shutting down them, they 
will be removed from heap too).

My queries created before by some other algorithms, written in a file, and 
then in experimental setup, I construct them as a Neo4j instance and use 
them one by one.

you can write your answer under 
*http://stackoverflow.com/questions/35876057/neo4j-java-api-gc-overhead-limit-exceeded-after-running-multiple-queries*
 
<http://stackoverflow.com/questions/35876057/neo4j-java-api-gc-overhead-limit-exceeded-after-running-multiple-queries>,
 
then I can select your answer as the one. 

Thanks.

On Thursday, March 24, 2016 at 11:25:30 PM UTC-7, Mohammad Hossain Namaki 
wrote:
>
> Hi all,
> I'm using neo4j.2.3.0.
> I'm running some experiments (over ~1000 graph queries) on the Neo4j Java 
> API. I don't use the cypher for that. So, I have my own algorithm. After 
> running around 100/200 queries, I'm getting the "GC Overhead Limit 
> Exceeded". I think there is something wrong with "
> org.neo4j.io.pagecache.impl.muninn.MuninnPageCache". 
>
> *Is there anyway to bound this cache size in Java API? or disable it?*
>
> I've already used this:
>
> knowledgeGraph = new GraphDatabaseFactory().newEmbeddedDatabaseBuilder(
> MODELGRAPH_DB_PATH)
>
> .*setConfig(GraphDatabaseSettings.pagecache_memory, "500M")*
> .newGraphDatabase();
>
> but it didn't work.
>
>
> Every time, I open a nested transaction for both query/data graphs and I 
> success/close them after finishing each query.
>
>
> I've used -Xmx12g -Xms12g as VM arguments and my machine has 16GB memory. 
> The data graph itself has 4.00 GB volume on the disk.
>
>
> Could you please help me on that?
>
>
> Thanks
>
>
>
>
>

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