[Neo4j] Neo4j Java API: GC overhead limit exceeded after running multiple queries

2016-03-08 Thread Mohammad Hossain Namaki
I’m using *Neo4j 2.3.0* in *Java*. I have 16 GB RAM, running the code on MAC OSX Laptop, using "*-Xmx12g -Xms12g*" as VM arguments. I’ve encountered a “GC overhead limit exceeded” problem in Neo4j Java API. In order to do experiments with lots of queries, I have a program which opens a

[Neo4j] Re: GC Overhead Limit Exceeded - Bounding the cache size

2016-03-28 Thread Mohammad Hossain Namaki
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

[Neo4j] GC Overhead Limit Exceeded - Bounding the cache size

2016-03-25 Thread Mohammad Hossain Namaki
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 "

[Neo4j] Re: GC Overhead Limit Exceeded - Bounding the cache size

2016-03-25 Thread Mohammad Hossain Namaki
, 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 Overhea

[Neo4j] Re: GC Overhead Limit Exceeded - Bounding the cache size

2016-03-27 Thread Mohammad Hossain Namaki
: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 ge

[Neo4j] Re: GC Overhead Limit Exceeded - Bounding the cache size

2016-03-25 Thread Mohammad Hossain Namaki
) at wsu.eecs.mlkd.KGQuery.machineLearningQuerying.BeamSearchRunner.initialize(BeamSearchRunner.java:248) at wsu.eecs.mlkd.KGQuery.machineLearningQuerying.BeamSearchRunner.main(BeamSearchRunner.java:439) On Thursday, March 24, 2016 at 11:25:30 PM UTC-7, Mohammad Hossain Namaki wrote: > > Hi all, > I'm using ne

[Neo4j] Re: Importing DBLP into Neo4j, the database doesn't start....

2016-04-29 Thread Mohammad Hossain Namaki
When I see inside of the index directory it has just "segments_1" and "segments.gen". How can I make some index over the labels of a created graph? On Thursday, April 28, 2016 at 12:37:42 PM UTC-7, Mohammad Hossain Namaki wrote: > > Dear all, > Hi, > I've wrote a j

[Neo4j] Re: Importing DBLP into Neo4j, the database doesn't start....

2016-05-02 Thread Mohammad Hossain Namaki
Hi Dear Michael, Sorry, I cannot understand this: "You are not supposed to set the pagesize And leave off that cache capacity" It means that I should remove those lines related to set the pageSize and cacheSize? Thanks. On Thursday, April 28, 2016 at 12:37:42 PM UTC-7, Mohamm

[Neo4j] Simulating Streaming Graph Databases with Neo4j

2016-06-29 Thread Mohammad Hossain Namaki
Hi, I want to use Neo4j in a streaming graph database which by the time nodes/edges are inserted/removed. However, as you know "dataGraph.createNode()" and "srcNode .createRelationshipTo(destNode, RelationshipType.withName(relationship))" are slow operations. How I can simulate streaming graph

[Neo4j] Update internal node Ids to be a sequence

2016-09-25 Thread Mohammad Hossain Namaki
Dear programmers, Hi, I have a requirement to have all node Id's in the graph database started from 0[max Number Of Nodes]. I won't add/remove any node after I create the initial graph database. Right now, I have a graph database that is not like that so node Id's are like

[Neo4j] Neo4j import in new versions on Mac

2016-10-04 Thread Mohammad Hossain Namaki
Dear all Neo4j Programmers, Hi, I am a Mac user having Neo4j 3.0 on my laptop. I want to use "neo4j-import" as I've used it in previous versions to import graphs. I've found it in "Application" directory. Then, by "showing package content", I've reached to the Neo4j-import. However, when I

Re: [Neo4j] Too many open files on a huge dataset with 110 labels

2016-10-06 Thread Mohammad Hossain Namaki
> Michael > > On Wed, Oct 5, 2016 at 5:24 AM, Mohammad Hossain Namaki <mhn@gmail.com > > wrote: > >> Hi, >> I've imported a huge dataset into Neo4j. 33M nodes and 144M >> relationships. Thanks to Neo4j makers, "neo4j-importer" was very

Re: [Neo4j] Too many open files on a huge dataset with 110 labels

2016-10-06 Thread Mohammad Hossain Namaki
6 at 7:58 PM, Mohammad Hossain Namaki <mhn@gmail.com > > wrote: > >> Thanks. >> So, there is no way that I can turn-off this indexing? My conjecture is >> Neo4j is a disk-based database management system and it should use bounded >> resources. If I have m

Re: [Neo4j] Too many open files on a huge dataset with 110 labels

2016-10-07 Thread Mohammad Hossain Namaki
is the dataset and when / how do you import it? > > Did you try to delete the schema/labels folder (it is rebuilt) > > On Fri, Oct 7, 2016 at 2:23 AM, Mohammad Hossain Namaki <mhn@gmail.com > > wrote: > >> >> Version 3.0.1 >> >> Sorry, I didn't get

[Neo4j] Re: Too many open files on a huge dataset with 110 labels

2016-10-07 Thread Mohammad Hossain Namaki
I've removed the label folder and run it again. I was watching the folder. it first created a lot of files then removed all of them and created just 14 items including write.lock and segments_1. but again at this line, I've got the error. FileOutputStream fos = new FileOutputStream(fout); I'll

[Neo4j] Too many open files on a huge dataset with 110 labels

2016-10-04 Thread Mohammad Hossain Namaki
Hi, I've imported a huge dataset into Neo4j. 33M nodes and 144M relationships. Thanks to Neo4j makers, "neo4j-importer" was very efficient. However, I'm getting (Too many open files) errors. ... Caused by: java.nio.file.FileSystemException: /fastscratch/mnamaki/idsForExp/idsAttackDB/schema/

[Neo4j] Re: Too many open files on a huge dataset with 110 labels

2016-10-16 Thread Mohammad Hossain Namaki
In total 110 distinct labels for all nodes. So, each label has a large number of corresponding nodes in datagraph. The problem was originally from my code. On Tuesday, October 4, 2016 at 8:24:52 PM UTC-7, Mohammad Hossain Namaki wrote: > > Hi, > I've imported a huge dataset into N