Java crash for sparql query with UNION on rdf:type

[bgad...@intec.ugent.be]

Hi,

I'm not sure why but a crash occurs when I execute the following query against stardog 2.0.3. I'm using CLI to execute the query. It's the stardog server process where the crash occurs.

PREFIX : <http://www.ugent.be/chest#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX temp: <http://swrl.stanford.edu/ontologies/built-ins/3.3/temporal.owl#>
select ?adm ?inf ?temp ?sput
where {
        ?inf rdf:type :RespiratoryInfection .
        ?inf :isInfectionOf ?adm .
        ?inf :isTreatedBy ?treatment .
        ?adm :hasBodyTemperature ?temp .
        ?temp temp:hasTime ?temptime .
        ?adm :hasSputumValue ?sput .
        {?sput rdf:type :NoSputum} union {?sput rdf:type :OneSputum} .
        ?sput :hasInsertTime ?sputtime .
        ?sput :hasSputumHoeveelheid ?hoev .
        ?inf :hasInfectionStart ?infstart .
        ?inf :hasInfectionEnd ?infend .
        ?treatment rdf:type :AntibioticTreatment .
        FILTER(
                ?sputtime <= ?infend &&
                ?sputtime >= ?infstart &&
                ?temptime <= ?infend &&
                ?temptime >= ?infstart
        )
}

The problem seems to be the union of rdf type statements. If I execute the query keeping only one of the union parts then I get no results for NoSputum and 130527 results for the OneSputum version.

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f9a2195e467, pid=12447, tid=140299794564864
#
# JRE version: Java(TM) SE Runtime Environment (7.0_51-b13) (build 1.7.0_51-b13)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.51-b03 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V  [libjvm.so+0x87b467]  oopDesc* PSPromotionManager::copy_to_survivor_space<false>(oopDesc*)+0x177
#
# Core dump written. Default location: /var/stardog-2.0.3/bin/core or core.12447
#
# An error report file with more information is saved as:
# /var/stardog-2.0.3/bin/hs_err_pid12447.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.sun.com/bugreport/crash.jsp
#

As an attachment I've also added the ontology and the hs_err_pid12447.log file.

Any ideas here?

With kind regards
Bram Gadeyne

[Mike Grove]

Have you tried with the latest version of Stardog?

Cheers,

Mike

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[Bram Gadeyne]

Yes,

It's the same result.

I've changed the -Xmx6g property to -Xmx4g. Now it does not crash anymore but it also does not return a result set.

Should I try openjdk in stead of oracle jdk? I'm using jdk 7u51 for 64 bit servers on Ubuntu 12.04.

Bram Gadeyne
Department of Information Technology
Internet Based Communication Networks and Services (IBCN)
Ghent University - iMinds 
Gaston Crommenlaan 8 (Bus 201), B-9050 Gent, Belgium
T: +32 (0)9 33 20497
T Secr: +32 (0)9 33 14900
F: +32 (0)9 33 14899
E: bram.g...@intec.UGent.be
W : www.ibcn.intec.UGent.be

Mike Grove schreef op 2/17/2014 1:12 PM:

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[Mike Grove]

On Mon, Feb 17, 2014 at 8:07 AM, Bram Gadeyne <bram.g...@intec.ugent.be> wrote:

Yes,

It's the same result.

There's no reason why it should crash, but we cannot look into it without the dataset to reproduce.

Also, are you using SL reasoning to execute the query?

 

I've changed the -Xmx6g property to -Xmx4g. Now it does not crash anymore but it also does not return a result set.

Should I try openjdk in stead of oracle jdk? I'm using jdk 7u51 for 64 bit servers on Ubuntu 12.04.

No, we recommend the Oracle JDK.  You might try a Java 6 JDK to see if it makes a difference.

 

Cheers,

Mike

[Bram Gadeyne]

Hi,

I've now also changed the java version to oracle jdk 6 update 45. But this has the same result.

I'm using SL reasoning to execute the query.

Bram Gadeyne
Department of Information Technology
Internet Based Communication Networks and Services (IBCN)
Ghent University - iMinds 
Gaston Crommenlaan 8 (Bus 201), B-9050 Gent, Belgium
T: +32 (0)9 33 20497
T Secr: +32 (0)9 33 14900
F: +32 (0)9 33 14899
E: bram.g...@intec.UGent.be
W : www.ibcn.intec.UGent.be

Mike Grove schreef op 2/17/2014 2:23 PM:

[Mike Grove]

Can you provide an example that reproduces the issue with the most recent version of Stardog?

Cheers,

Mike

[Bram Gadeyne]

Hi Mike,

I'm sorry but I've made some changes to my ontology and data and now the problem does not occur any more. I don't have a backup from when it did.

If I encounter it again I'll try and make a backup so you can reproduce the problem.

With kind regards

Bram Gadeyne
Department of Information Technology
Internet Based Communication Networks and Services (IBCN)
Ghent University - iMinds 
Gaston Crommenlaan 8 (Bus 201), B-9050 Gent, Belgium
T: +32 (0)9 33 20497
T Secr: +32 (0)9 33 14900
F: +32 (0)9 33 14899
E: bram.g...@intec.UGent.be
W : www.ibcn.intec.UGent.be

Mike Grove schreef op 2/18/2014 8:08 PM:

[Mike Grove]

On Wed, Feb 19, 2014 at 2:36 AM, Bram Gadeyne <bram.g...@intec.ugent.be> wrote:

Hi Mike,

I'm sorry but I've made some changes to my ontology and data and now the problem does not occur any more. I don't have a backup from when it did.

Great, thanks for the update.

Good luck with the work.

Cheers,

Mike