Settings Java heap memory

[Parthasarathi Mukhopadhyay]

Dear all

By following the system guide of VocBench, I set the following values inside /vocbench3-10.2.1-full/semanticturkey-10.2.1/bin/setenv file (am using an i7 processor based machine with 16 GB RAM and 64 bit Ubuntu LTS 22.04):

export GDB_MAX_MEM=6144M
export GDB_MIN_MEM=2048M
export JAVA_MAX_MEM=2048M
export JAVA_MIN_MEM=256M

This settings worked for me in an earlier occasion of importing the entire Agrovoc, but today reported an out of memory error when I attempted to import MeSH (2.3 GB NT file).

Am I using the right place / file to set  the heap memory? If yes, what should be the right size in the above stated configuration?

Regards

Parthasarathi Mukhopadhyay Professor, Department of Library and Information Science, University of Kalyani, Kalyani - 741 235 (WB), India

[Armando Stellato]

Dear Parthasarathi,

 

could you provide us a description of the configuration of your project?

 

For instance, I’m assuming that you are really using GraphDB for loading MeSH, so using a remote project, using the GraphDB sail (free or SE depends on the license you are using) etc..

 

Could you verify this? I suppose 6Gb given to GDB even for that amount (2.3Gb) should be enough. In negative case, you could try raising GDB’s heap to 8 or 10, but I don’t really think they are necessary

 

Kind Regards,

 

Armando

 

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[Parthasarathi Mukhopadhyay]

Thanks Armando.

I'm using GraphDB free version (graphdb-free-9.8.1) at the backend and using CreateRemote function of VocBench.

The other things that may be important

1. I set skos for both model and lexicalization for MeSH.

2.  It is producing error like this (we again performed it to report here the exact message) at GraphDB end -

[INFO ] 2022-06-09 02:07:07,986 [repositories/MeSH_core | o.e.r.h.s.r.t.TransactionController] PUT txn operation request finished.
[INFO ] 2022-06-09 02:07:07,988 [repositories/MeSH_core | o.e.r.h.s.r.t.TransactionController] PUT txn query request
[WARN ] 2022-06-09 02:17:38,098 [repositories/MeSH_core | o.e.r.h.s.r.t.ActiveTransactionRegistry] deregistered expired transaction 3bd45905-8af9-4525-8f98-302481aa7912
[WARN ] 2022-06-09 02:17:38,098 [repositories/MeSH_core | o.e.r.h.s.r.t.ActiveTransactionRegistry] deregistered expired transaction cd2e640e-81a5-4706-a6d9-191d8c7b51ad
[WARN ] 2022-06-09 02:17:38,098 [repositories/MeSH_core | o.e.r.h.s.r.t.ActiveTransactionRegistry] deregistered expired transaction af079a03-f7ef-4a01-a94b-34c70aec309f
java.lang.OutOfMemoryError: Java heap space
Dumping heap to /home/roshni/graphdb-free-9.8.1/heapdump.hprof ...
Heap dump file created [5191852875 bytes in 24.345 secs]
#
# java.lang.OutOfMemoryError: Java heap space
# -XX:OnOutOfMemoryError="kill -9 %p"
#   Executing /bin/sh -c "kill -9 29395"...
Killed

3. And a connection refused error at the VocBench end -

org.apache.http.conn.HttpHostConnectException: Connect to localhost:7200 [localhost/127.0.0.1] failed: Connection refused (Connection refused)

Details:

4 I'm using the same machine here for VocBench and Skosmos, and transferring data from VocBench to Skosmos for retrieval by end users. But unfortunately these two sets of software have different Java versions requirements - Skosmos requires Java 11 and VoCBench needs Java 8.

I set Java 11 as the option -

update-java-alternatives -l
java-1.11.0-openjdk-amd64      1111       /usr/lib/jvm/java-1.11.0-openjdk-amd64
java-1.8.0-openjdk-amd64       1081       /usr/lib/jvm/java-1.8.0-openjdk-amd64

and calling VocBench from a script like this -

export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/
echo "Setting Java_Home ...."
sleep 2s
echo $JAVA_HOME
sleep 2s
echo "Starting Vocbench ......"
./start
sleep 2s
echo "Showing status ...."
./status
sleep 3s
echo "Click to open Vocbench - http://localhost:1979/vocbench3/#/Home"
echo " "

My setenv memory statements are -

# export KARAF_NOROOT # Prevent execution as root if set to true

export GDB_MAX_MEM=6144M
export GDB_MIN_MEM=2048M
export JAVA_MAX_MEM=2048M
export JAVA_MIN_MEM=256M

A check of heap memory shows  (I think my heap memory statements are not honoured at all) -

$ jps -l

29395 com.ontotext.graphdb.server.GraphDBWorkbench
40021 org.apache.karaf.main.Main
41627 jdk.jcmd/sun.tools.jps.Jps

$ jstat -gc 40021
 S0C    S1C    S0U    S1U      EC       EU        OC         OU       MC     MU    CCSC   CCSU   YGC     YGCT    FGC    FGCT    CGC    CGCT     GCT  
423936.0 440320.0  0.0    0.0   465408.0 286227.5  589312.0   220325.9  116736.0 105830.9 16640.0 13756.5     27    1.534   5      0.722   -          -    2.256

Plz guide and let me know if any other info is needed ...

Regards

[Roland Wingerter]

Hi,

for running Java 8 / Java 11 concurrently check out this message by Armando:

https://groups.google.com/g/vocbench-user/c/IlnuRGLLI0Q/m/1Fl6KkacAQAJ

Kind regards

Roland