My JVM properties include
# Enter one VM parameter per line, note that some parameters can only be
set once.
# For example, to adjust the maximum memory usage to 512 MB, uncomment the
following line
-Xmx6144m
Xmx4G -Xms4G -Xmn1G
but still i am getting GC overhead limit exceeded error. (I have tried
from 512m to 6GB)
My neo4j.propertie file contains
neostore.nodestore.db.mapped_memory=100M
neostore.relationshipstore.db.mapped_memory=2G
neostore.propertystore.db.mapped_memory=200M
neostore.propertystore.db.strings.mapped_memory=200M
neostore.propertystore.db.arrays.mapped_memory=0M
Any more suggestions to get rid of the error
On Wed, Jun 25, 2014 at 6:34 PM, Pavan Kumar <kumar.pavan...@gmail.com>
wrote:
> My property file is
>
> # Default values for the low-level graph engine
>
> neostore.nodestore.db.mapped_memory=100M
> neostore.relationshipstore.db.mapped_memory=2G
> neostore.propertystore.db.mapped_memory=200M
> neostore.propertystore.db.strings.mapped_memory=200M
> neostore.propertystore.db.arrays.mapped_memory=0M
>
> # Enable this to be able to upgrade a store from an older version
> allow_store_upgrade=true
>
> # Enable this to specify a parser other than the default one.
> #cypher_parser_version=2.0
>
> # Keep logical logs, helps debugging but uses more disk space, enabled for
> # legacy reasons To limit space needed to store historical logs use values
> such
> # as: "7 days" or "100M size" instead of "true"
> keep_logical_logs=true
>
> # Autoindexing
>
> # Enable auto-indexing for nodes, default is false
> #node_auto_indexing=true
>
> # The node property keys to be auto-indexed, if enabled
> #node_keys_indexable=name,age
>
> # Enable auto-indexing for relationships, default is false
> #relationship_auto_indexing=true
>
> # The relationship property keys to be auto-indexed, if enabled
> #relationship_keys_indexable=name,age
> cache_type=strong
>
>
>
> My jvm options are
> # Enter one VM parameter per line, note that some parameters can only be
> set once.
> # For example, to adjust the maximum memory usage to 512 MB, uncomment the
> following line
> -Xmx512m
>
> But still i am getting GC overhead limit exceeded error
> Kindly somebody suggest me
>
> On Wed, Jun 25, 2014 at 5:01 PM, Michael Hunger <
> michael.hun...@neotechnology.com> wrote:
>
>> use 1000 here
>> USING PERIODIC COMMIT 1000
>>
>> Increase the memory settings to 6G
>>
>> As you run on windows:
>>
>> neostore.nodestore.db.mapped_memory=100M
>> neostore.relationshipstore.db.mapped_memory=2G
>> neostore.propertystore.db.mapped_memory=200M
>> neostore.propertystore.db.strings.mapped_memory=200M
>> neostore.propertystore.db.arrays.mapped_memory=0M
>>
>> also can you share your complete CSV with me privately?
>>
>> Do you have any nodes in your dataset that have many (100k-1M) of
>> relationships?
>>
>> On Wed, Jun 25, 2014 at 1:23 PM, Pavan Kumar <kumar.pavan...@gmail.com>
>> wrote:
>>
>>> Hi ,
>>> My qiuery is as follows
>>> create constraint on (ChemicalName:chemicalname) assert
>>> ChemicalName.chemicalname is unique;
>>> create constraint on (ChemicalID:chemicalid) assert
>>> ChemicalID.chemicalid is unique;
>>> create constraint on (Genesymbol:genesymbol) assert
>>> Genesymbol.genesymbol is unique;
>>> create constraint on (Geneid:geneid) assert Geneid.geneid is unique;
>>> create constraint on (Geneform:geneform) assert Geneform.geneform is
>>> unique;
>>> create constraint on (Interaction:interaction) assert
>>> Interaction.interaction is unique;
>>> create constraint on (Interactionactions:interactionactions) assert
>>> Interactionactions.interactionactions is unique;
>>> create constraint on (PubmedID:pubmed) assert PubmedID.pubmed is unique;
>>> create index on :ChemicalName(chemicalname);
>>> create index on :ChemicalID(chemicalid);
>>> create index on :Genesymbol(genesymbol);
>>> create index on :Geneid(geneid);
>>> create index on :Geneform(geneform);
>>> create index on :Interaction(interaction);
>>> create index on :Interactionactions(interactionactions);
>>> create index on :PubmedID(pubmed);
>>>
>>> USING PERIODIC COMMIT 10000
>>> LOAD CSV WITH HEADERS FROM
>>> "file:D:/Graph_Database/CTD/CTD_chem_gene_ixns.csv"
>>> AS chemgeneinteractions
>>> match (geneid:Geneid{geneid: chemgeneinteractions.GeneID})
>>> match (genesymbol:Genesymbol{genesymbol:
>>> chemgeneinteractions.GeneSymbol})
>>> merge (chemicalname:ChemicalID{chemicalid:
>>> chemgeneinteractions.ChemicalID, chemicalname:
>>> chemgeneinteractions.ChemicalName})
>>> ON CREATE SET
>>> chemicalname.chemicalid=chemgeneinteractions.ChemicalID,chemicalname.chemicalid=chemgeneinteractions.ChemicalName
>>> merge (geneform:Geneform {geneform: chemgeneinteractions.GeneForms})
>>> merge (interations:Interaction{interact:
>>> chemgeneinteractions.Interaction})
>>> merge (oraganism:Organism{organism: chemgeneinteractions.Organism})
>>> merge (interaction:Interactionactions{interr:
>>> chemgeneinteractions.InteractionActions})
>>> merge (pubmed:PubmedID{pub: chemgeneinteractions.PubMedIDs})
>>> merge (geneid)-[:Gene_Symbol]->(genesymbol)
>>> merge (geneid)-[:chemicalname]->(chemicalname)
>>> merge (geneid)-[:geneform]->(genefrom)
>>> merge (geneid)-[:Its_interaction_action]->(interactions)
>>> merge (geneid)-[:Its_interaction]->(interaction)
>>> merge (geneid)-[:PubmedID]->(pubmed)
>>> merge (geneid)-[:Related_To]->(organism)
>>> merge (genesymbol)-[:chemicalname]->(chemicalname)
>>> merge (genesymbol)-[:geneform]->(genefrom)
>>> merge (genesymbol)-[:geneform]->(genefrom)
>>> merge (genesymbol)-[:Its_interaction_action]->(interactions)
>>> merge (genesymbol)-[:Its_interaction]->(interaction)
>>> merge (genesymbol)-[:PubmedID]->(pubmed)
>>> merge (genesymbol)-[:Related_To]->(organism)
>>>
>>>
>>>
>>> My jvm properties are
>>> -Xmx512m
>>> -XX:+UseConcMarkSweepGC
>>>
>>>
>>>
>>>
>>> On Wed, Jun 25, 2014 at 4:49 PM, Michael Hunger <
>>> michael.hun...@neotechnology.com> wrote:
>>>
>>>> Please read this blog post:
>>>> http://jexp.de/blog/2014/06/load-csv-into-neo4j-quickly-and-successfully/
>>>>
>>>> And yes you should use more memory than 512 byte.
>>>>
>>>> -Xmns4G -Xmx4G -Xmn1G
>>>>
>>>>
>>>> On Wed, Jun 25, 2014 at 1:17 PM, Michael Hunger <
>>>> michael.hun...@neotechnology.com> wrote:
>>>>
>>>>> What does your query look like?
>>>>> Please switch to Neo4j 2.1.2
>>>>>
>>>>> And create indexes / constraints for the nodes you're inserting with
>>>>> merge or looking up via MATCH.
>>>>>
>>>>>
>>>>> Am 18.06.2014 um 08:46 schrieb Pavan Kumar <kumar.pavan...@gmail.com>:
>>>>>
>>>>> Hi,
>>>>> I have deployed neo4j 2.1.0-M01 on windows which has 8GB RAM. I am
>>>>> trying to import CSV file which has 30000 records. I am using USING
>>>>> PERIODIC COMMIT 1000 LOAD CSV command for importing, but it gives
>>>>> unknown error. I have modified neo4j.properties file as adviced in the
>>>>> blogs. My neo4j.properties now looks like
>>>>> # Default values for the low-level graph engine
>>>>>
>>>>> neostore.nodestore.db.mapped_memory=200M
>>>>> neostore.relationshipstore.db.mapped_memory=4G
>>>>> neostore.propertystore.db.mapped_memory=500M
>>>>> neostore.propertystore.db.strings.mapped_memory=500M
>>>>> neostore.propertystore.db.arrays.mapped_memory=500M
>>>>>
>>>>> # Enable this to be able to upgrade a store from an older version
>>>>> allow_store_upgrade=true
>>>>>
>>>>> # Enable this to specify a parser other than the default one.
>>>>> #cypher_parser_version=2.0
>>>>>
>>>>> # Keep logical logs, helps debugging but uses more disk space, enabled
>>>>> for
>>>>> # legacy reasons To limit space needed to store historical logs use
>>>>> values such
>>>>> # as: "7 days" or "100M size" instead of "true"
>>>>> keep_logical_logs=true
>>>>>
>>>>> # Autoindexing
>>>>>
>>>>> # Enable auto-indexing for nodes, default is false
>>>>> node_auto_indexing=true
>>>>>
>>>>> # The node property keys to be auto-indexed, if enabled
>>>>> #node_keys_indexable=name,age
>>>>>
>>>>> # Enable auto-indexing for relationships, default is false
>>>>> relationship_auto_indexing=true
>>>>>
>>>>> # The relationship property keys to be auto-indexed, if enabled
>>>>> #relationship_keys_indexable=name,age
>>>>>
>>>>> # Setting for Community Edition:
>>>>> cache_type=weak
>>>>>
>>>>> Still i am facing the same problem. Is there any other file to change
>>>>> properties. Kindly help me in this issue.
>>>>> Thanks in advance
>>>>>
>>>>> On Tuesday, 4 March 2014 21:24:03 UTC+5:30, Aram Chung wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I was asked to post this here by Mark Needham (@markhneedham) who
>>>>>> thought my query took longer than it should.
>>>>>>
>>>>>> I'm trying to see how graph databases could be used in investigative
>>>>>> journalism: I was loading in New York State's Active Corporations:
>>>>>> Beginning 1800 data from https://data.ny.gov/Economic-
>>>>>> Development/Active-Corporations-Beginning-1800/n9v6-gdp6 as a
>>>>>> 1964486-row csv (and deleted all U+F8FF characters, because I was getting
>>>>>> "[null] is not a supported property value"). The Cypher query I used was
>>>>>>
>>>>>> USING PERIODIC COMMIT 500
>>>>>> LOAD CSV
>>>>>> FROM "file://path/to/csv/Active_Corporations___Beginning_1800_
>>>>>> _without_header__wonky_characters_fixed.csv"
>>>>>> AS company
>>>>>> CREATE (:DataActiveCorporations
>>>>>> {
>>>>>> DOS_ID:company[0],
>>>>>> Current_Entity_Name:company[1],
>>>>>> Initial_DOS_Filing_Date:company[2],
>>>>>> County:company[3],
>>>>>> Jurisdiction:company[4],
>>>>>> Entity_Type:company[5],
>>>>>>
>>>>>> DOS_Process_Name:company[6],
>>>>>> DOS_Process_Address_1:company[7],
>>>>>> DOS_Process_Address_2:company[8],
>>>>>> DOS_Process_City:company[9],
>>>>>> DOS_Process_State:company[10],
>>>>>> DOS_Process_Zip:company[11],
>>>>>>
>>>>>> CEO_Name:company[12],
>>>>>> CEO_Address_1:company[13],
>>>>>> CEO_Address_2:company[14],
>>>>>> CEO_City:company[15],
>>>>>> CEO_State:company[16],
>>>>>> CEO_Zip:company[17],
>>>>>>
>>>>>> Registered_Agent_Name:company[18],
>>>>>> Registered_Agent_Address_1:company[19],
>>>>>> Registered_Agent_Address_2:company[20],
>>>>>> Registered_Agent_City:company[21],
>>>>>> Registered_Agent_State:company[22],
>>>>>> Registered_Agent_Zip:company[23],
>>>>>>
>>>>>> Location_Name:company[24],
>>>>>> Location_Address_1:company[25],
>>>>>> Location_Address_2:company[26],
>>>>>> Location_City:company[27],
>>>>>> Location_State:company[28],
>>>>>> Location_Zip:company[29]
>>>>>> }
>>>>>> );
>>>>>>
>>>>>> Each row is one node so it's as close to the raw data as possible.
>>>>>> The idea is loosely that these nodes will be linked with new nodes
>>>>>> representing people and addresses verified by reporters.
>>>>>>
>>>>>> This is what I got:
>>>>>>
>>>>>> +-------------------+
>>>>>> | No data returned. |
>>>>>> +-------------------+
>>>>>> Nodes created: 1964486
>>>>>> Properties set: 58934580
>>>>>> Labels added: 1964486
>>>>>> 4550855 ms
>>>>>>
>>>>>> Some context information:
>>>>>> Neo4j Milestone Release 2.1.0-M01
>>>>>> Windows 7
>>>>>> java version "1.7.0_03"
>>>>>>
>>>>>> Best,
>>>>>> Aram
>>>>>>
>>>>>
>>>>> --
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>>>>>
>>>>>
>>>>>
>>>> --
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>>>>
>>>
>>>
>>>
>>> --
>>> Thanks & Regards,
>>> Pavan Kumar
>>> Project Engineer
>>> CDAC -KP
>>> Ph +91-7676367646
>>>
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>>
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>
>
>
> --
> Thanks & Regards,
> Pavan Kumar
> Project Engineer
> CDAC -KP
> Ph +91-7676367646
>
--
Thanks & Regards,
Pavan Kumar
Project Engineer
CDAC -KP
Ph +91-7676367646
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