[protege-owl] Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

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[protege-owl] Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Julia Dmitrieva

Hello,

I am using protege owl plugin API in mijn java eclipce
application. I try to download  NCI Thesaurus.owl file
with the following snip code:

String uri = "file:///tralala/Thesaurus.owl";
                StringBuffer html = new StringBuffer(HEADER);
                StringBuffer detail = new StringBuffer();
               
                try {
                        OWLModel owlModel = ProtegeOWL.createJenaOWLModelFromURI
(uri);
                        html.append(getClassList(owlModel));


This file is 70M and after some time I get the following problem.

CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows 2000,
encoding=UTF-8, language=en, country=US
WARNING: Plugins directory not found: C:\Program Files\eclipse3.0
\workspace\OwlDataMiner\plugins -- PluginUtilities.findPluginsDirectory()
[ProtegeOWLParser] Triple 10000
[ProtegeOWLParser] Triple 20000
[ProtegeOWLParser] Triple 30000
[ProtegeOWLParser] Triple 40000
[ProtegeOWLParser] Triple 50000
[ProtegeOWLParser] Triple 60000
[ProtegeOWLParser] Triple 70000
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space


You help will be very appriciated.
Julia

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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Tania Tudorache
See this:

http://protege.cim3.net/cgi-bin/wiki.pl?ScalabilityAndTuning

Tania

Julia wrote:

>Hello,
>
>I am using protege owl plugin API in mijn java eclipce
>application. I try to download  NCI Thesaurus.owl file
>with the following snip code:
>
>String uri = "file:///tralala/Thesaurus.owl";
> StringBuffer html = new StringBuffer(HEADER);
> StringBuffer detail = new StringBuffer();
>
> try {
> OWLModel owlModel = ProtegeOWL.createJenaOWLModelFromURI
>(uri);
> html.append(getClassList(owlModel));
>
>
>This file is 70M and after some time I get the following problem.
>
>CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows 2000,
>encoding=UTF-8, language=en, country=US
>WARNING: Plugins directory not found: C:\Program Files\eclipse3.0
>\workspace\OwlDataMiner\plugins -- PluginUtilities.findPluginsDirectory()
>[ProtegeOWLParser] Triple 10000
>[ProtegeOWLParser] Triple 20000
>[ProtegeOWLParser] Triple 30000
>[ProtegeOWLParser] Triple 40000
>[ProtegeOWLParser] Triple 50000
>[ProtegeOWLParser] Triple 60000
>[ProtegeOWLParser] Triple 70000
>Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
>
>
>You help will be very appriciated.
>Julia
>
>-------------------------------------------------------------------------
>To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>
>  
>

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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Julia Dmitrieva
Hello Tania,

Thank you for answer,
the problem is that I try to use Protege OWL API
in my Java application in eclipse and not in
Protege self. When I try to download Thesaurus.owl
file I see CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M
but in the file Eclipse.ini I have set the the VM options with:
-vmargs
-Xms1024m
-Xmx1024m

I have tryed also to download my thesaurus.owl file with Protege 3.2
beta, but the result is the same.
What I find very strange, that my Java program still try to use
66M memory, but I have set it to 1M.
My computer has 514M physical memory and the files where I
would like to work with are 100M.
Is it possible to solve my problem in some way. Or is there are
some parser for OWL like SAX parser for xml.


Thanks in advance,
with best regards Julia.


Tania Tudorache wrote:

> See this:
>
> http://protege.cim3.net/cgi-bin/wiki.pl?ScalabilityAndTuning
>
> Tania
>
> Julia wrote:
>
>> Hello,
>>
>> I am using protege owl plugin API in mijn java eclipce
>> application. I try to download  NCI Thesaurus.owl file
>> with the following snip code:
>>
>> String uri = "file:///tralala/Thesaurus.owl";
>>         StringBuffer html = new StringBuffer(HEADER);
>>         StringBuffer detail = new StringBuffer();
>>        
>>         try {
>>             OWLModel owlModel = ProtegeOWL.createJenaOWLModelFromURI
>> (uri);
>>             html.append(getClassList(owlModel));
>>
>>
>> This file is 70M and after some time I get the following problem.
>>
>> CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows
>> 2000, encoding=UTF-8, language=en, country=US
>> WARNING: Plugins directory not found: C:\Program Files\eclipse3.0
>> \workspace\OwlDataMiner\plugins -- PluginUtilities.findPluginsDirectory()
>> [ProtegeOWLParser] Triple 10000
>> [ProtegeOWLParser] Triple 20000
>> [ProtegeOWLParser] Triple 30000
>> [ProtegeOWLParser] Triple 40000
>> [ProtegeOWLParser] Triple 50000
>> [ProtegeOWLParser] Triple 60000
>> [ProtegeOWLParser] Triple 70000
>> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
>>
>>
>> You help will be very appriciated.
>> Julia
>>
>> -------------------------------------------------------------------------
>> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>>
>>
>>  
>>
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>



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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Nikolaj Berntsen
Julia Dmitrieva wrote:

> Hello Tania,
>
> Thank you for answer,
> the problem is that I try to use Protege OWL API
> in my Java application in eclipse and not in
> Protege self. When I try to download Thesaurus.owl
> file I see CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M
> but in the file Eclipse.ini I have set the the VM options with:
> -vmargs
> -Xms1024m
> -Xmx1024m

-vmargs -Xmx512M -Xms128M -XX:PermSize=64M -XX:MaxPermSize=128M

is the options I give to eclipse, so if they have the same format, I
would say that you should use 'M' rather than 'm', and perhaps you can
benefit from the PermSize option as well.

Cheers,
/\/
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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Julia Dmitrieva
Hello Nikolai,

I have tryed it, the problem is just the same:
thus I still have:
CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows
2000, encoding=UTF-8, language=en, country=US

May be I am not understanding something important,
I am using owl API jar files as it is, without that
I built it or in my application. Can it be the
problem that somewhere in the OWL API is set that
the the memory usage must be 66M, not more.
May be it sounds very stupid, but ...

Julia

Nikolaj Berntsen wrote:

>
>
> -vmargs -Xmx512M -Xms128M -XX:PermSize=64M -XX:MaxPermSize=128M
>
> is the options I give to eclipse, so if they have the same format, I
> would say that you should use 'M' rather than 'm', and perhaps you can
> benefit from the PermSize option as well.
>
> Cheers,
> /\/
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html


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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Elyes Lehtihet-3

Hello Julia,

 

You should change the java heap size options by:

-opening 'YourDirectory/Protege_X.Y/Protege.lax'

-changing the initial/maximum heap size (according to your system spec.)

 

#   LAX.NL.JAVA.OPTION.JAVA.HEAP.SIZE.INITIAL

#   -----------------------------------------

#   initial heap size

 

lax.nl.java.option.java.heap.size.initial=10000000

 

 

#   LAX.NL.JAVA.OPTION.JAVA.HEAP.SIZE.MAX

#   -------------------------------------

#   maximum heap size

 

lax.nl.java.option.java.heap.size.max=500000000

 

 

Hope this helps,

Elyes

 

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Julia Dmitrieva
Sent: Monday, June 12, 2006 11:16 AM
To: [hidden email]
Subject: [protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

 

Hello Nikolai,

 

I have tryed it, the problem is just the same:

thus I still have:

CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows

2000, encoding=UTF-8, language=en, country=US

 

May be I am not understanding something important,

I am using owl API jar files as it is, without that

I built it or in my application. Can it be the

problem that somewhere in the OWL API is set that

the the memory usage must be 66M, not more.

May be it sounds very stupid, but ...

 

Julia

 

Nikolaj Berntsen wrote:

 

>

>

> -vmargs -Xmx512M -Xms128M -XX:PermSize=64M -XX:MaxPermSize=128M

>

> is the options I give to eclipse, so if they have the same format, I

> would say that you should use 'M' rather than 'm', and perhaps you can

> benefit from the PermSize option as well.

>

> Cheers,

> /\/

> -------------------------------------------------------------------------

> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html

 

 

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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Nikolaj Berntsen
In reply to this post by Julia Dmitrieva
Julia Dmitrieva wrote:

> Hello Nikolai,
>
> I have tryed it, the problem is just the same:
> thus I still have:
> CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows
> 2000, encoding=UTF-8, language=en, country=US
>
> May be I am not understanding something important,

my guess is that you don't set the options the right place. I have not
tried to pass parameters to protege, so I cannot help you out with this one.

Good luck,
/\/

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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Julia Dmitrieva
In reply to this post by Tania Tudorache
Hello,

I have no success with using OWL API for big files,
( with files from API examples such as
http://www.biopax.org/release/biopax-level2.owl
everething goes  OK)

I think that I need some parser that parse the
owl document like SAX XML parser.
This parser reads the document sequntially and issues calls to
special functions called handlers.
With this kind of parser I can try to split my big
owl file in parts and then I can use OWL API to work further.

Can you reccomend me something.
With best regards,
Julia
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[protege-owl] unsubscribe

karim bassil
In reply to this post by Julia Dmitrieva
Hello everybody

I am trying to unsubcribe for the mailing list,i m following the link and
doing what should be done but it doesn't seems to work.

Plz if someone can help just reply to me.

Sorry for the bothering and thx u.


>From: Julia Dmitrieva <[hidden email]>
>Reply-To: [hidden email]
>To: [hidden email]
>Subject: [protege-owl] Re: Exception in thread "main"
>java.lang.OutOfMemoryError: Java heap space
>Date: Mon, 12 Jun 2006 12:16:17 +0200
>
>Hello Nikolai,
>
>I have tryed it, the problem is just the same:
>thus I still have:
>CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows 2000,
>encoding=UTF-8, language=en, country=US
>
>May be I am not understanding something important,
>I am using owl API jar files as it is, without that
>I built it or in my application. Can it be the
>problem that somewhere in the OWL API is set that
>the the memory usage must be 66M, not more.
>May be it sounds very stupid, but ...
>
>Julia
>
>Nikolaj Berntsen wrote:
>
>>
>>
>>-vmargs -Xmx512M -Xms128M -XX:PermSize=64M -XX:MaxPermSize=128M
>>
>>is the options I give to eclipse, so if they have the same format, I
>>would say that you should use 'M' rather than 'm', and perhaps you can
>>benefit from the PermSize option as well.
>>
>>Cheers,
>>/\/
>>-------------------------------------------------------------------------
>>To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>
>-------------------------------------------------------------------------
>To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>


-------------------------------------------------------------------------
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[protege-owl] Re: unsubscribe

Jon Lea
In reply to this post by Julia Dmitrieva
I've been having the same problem so when you guys figure out why
unsubscribe doesn't work please take me off also.

Thanks.

Jon Lea
[hidden email]


-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of karim
bassil
Sent: Monday, June 12, 2006 8:00 AM
To: [hidden email]
Subject: [protege-owl] unsubscribe

Hello everybody

I am trying to unsubcribe for the mailing list,i m following the link
and
doing what should be done but it doesn't seems to work.

Plz if someone can help just reply to me.

Sorry for the bothering and thx u.


>From: Julia Dmitrieva <[hidden email]>
>Reply-To: [hidden email]
>To: [hidden email]
>Subject: [protege-owl] Re: Exception in thread "main"
>java.lang.OutOfMemoryError: Java heap space
>Date: Mon, 12 Jun 2006 12:16:17 +0200
>
>Hello Nikolai,
>
>I have tryed it, the problem is just the same:
>thus I still have:
>CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows
2000,

>encoding=UTF-8, language=en, country=US
>
>May be I am not understanding something important,
>I am using owl API jar files as it is, without that
>I built it or in my application. Can it be the
>problem that somewhere in the OWL API is set that
>the the memory usage must be 66M, not more.
>May be it sounds very stupid, but ...
>
>Julia
>
>Nikolaj Berntsen wrote:
>
>>
>>
>>-vmargs -Xmx512M -Xms128M -XX:PermSize=64M -XX:MaxPermSize=128M
>>
>>is the options I give to eclipse, so if they have the same format, I
>>would say that you should use 'M' rather than 'm', and perhaps you can
>>benefit from the PermSize option as well.
>>
>>Cheers,
>>/\/
>>----------------------------------------------------------------------
---
>>To unsubscribe go to
http://protege.stanford.edu/community/subscribe.html
>
>
>-----------------------------------------------------------------------
--
>To unsubscribe go to
http://protege.stanford.edu/community/subscribe.html
>


------------------------------------------------------------------------
-
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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Nick Drummond
In reply to this post by Julia Dmitrieva
Julia,

You should be able to handle loading the NCI Thesaurus.
I don't develop with Eclipse, I use IntelliJ but if you are running  
directly from an IDE there is normally a way of configuring the VM  
parameters (as Nikolaj says) used at runtime.

I just pass in a chunk of extra heap (depending on your machine's  
memory):
-Xmx500M

If you can't work out how to do this in the IDE, you might have to  
run directly from the classes, using java directly from a command  
prompt (and equally, add the extra memory).

Good luck

Nick


On 12 Jun 2006, at 13:50, Julia Dmitrieva wrote:

> Hello,
>
> I have no success with using OWL API for big files,
> ( with files from API examples such as http://www.biopax.org/ 
> release/biopax-level2.owl
> everething goes  OK)
>
> I think that I need some parser that parse the
> owl document like SAX XML parser.
> This parser reads the document sequntially and issues calls to
> special functions called handlers.
> With this kind of parser I can try to split my big
> owl file in parts and then I can use OWL API to work further.
>
> Can you reccomend me something.
> With best regards,
> Julia
> ----------------------------------------------------------------------
> ---
> To unsubscribe go to http://protege.stanford.edu/community/ 
> subscribe.html
>

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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Tania Tudorache
In reply to this post by Nikolaj Berntsen
Julia,

this is a Java VM argument that you need to set in the Eclipse Run (or
Debug) Configuration for your main class. I suppose you did not set this
in the correct place. See schreenshot from below.

And, one more important thing: You cannot set a bigger heap size than
the size of your physical memory. Please read this for more details:
http://protege.cim3.net/cgi-bin/wiki.pl?ScalabilityAndTuning

Try to set the heap size to 250M ("-Xmx250M").

Tania




Nikolaj Berntsen wrote:

>Julia Dmitrieva wrote:
>
>  
>
>>Hello Nikolai,
>>
>>I have tryed it, the problem is just the same:
>>thus I still have:
>>CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows
>>2000, encoding=UTF-8, language=en, country=US
>>
>>May be I am not understanding something important,
>>    
>>
>
>my guess is that you don't set the options the right place. I have not
>tried to pass parameters to protege, so I cannot help you out with this one.
>
>Good luck,
>/\/
>
>
>  
>

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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Julia Dmitrieva
Thank you Tania,

I dont see you screenshot, I sent you
my.
I think that I am doing it at the good place.
Probably my problem is only 512M of the physical
memory.

With best regards,
Julia


Tania Tudorache wrote:

> Julia,
>
> this is a Java VM argument that you need to set in the Eclipse Run (or
> Debug) Configuration for your main class. I suppose you did not set this
> in the correct place. See schreenshot from below.
>
> And, one more important thing: You cannot set a bigger heap size than
> the size of your physical memory. Please read this for more details:
> http://protege.cim3.net/cgi-bin/wiki.pl?ScalabilityAndTuning
>
> Try to set the heap size to 250M ("-Xmx250M").
>
> Tania
>
>
>
>
> Nikolaj Berntsen wrote:
>
>> Julia Dmitrieva wrote:
>>
>>  
>>
>>> Hello Nikolai,
>>>
>>> I have tryed it, the problem is just the same:
>>> thus I still have:
>>> CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows
>>> 2000, encoding=UTF-8, language=en, country=US
>>>
>>> May be I am not understanding something important,
>>>  
>>
>>
>> my guess is that you don't set the options the right place. I have not
>> tried to pass parameters to protege, so I cannot help you out with
>> this one.
>>
>> Good luck,
>> /\/
>>
>>
>>  
>>
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html

--
Julia Dmitrieva

LIACS Office:  124
Phone:  +31 (0)71 – 5275777
E-Mail:  [hidden email]

Member of:  Imaging
Scientific Personnel


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[protege-owl] Re: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Tania Tudorache
Yes, it is the right place. In my Eclipse environment, I only write in
the VM arguments:"-Xmx512M" without the other stuff (${env..}).

But, as I said, I think the problem is that you don't have enough
physical memory.

Tania


Julia Dmitrieva wrote:

> Thank you Tania,
>
> I dont see you screenshot, I sent you
> my.
> I think that I am doing it at the good place.
> Probably my problem is only 512M of the physical
> memory.
>
> With best regards,
> Julia
>
>
> Tania Tudorache wrote:
>
>> Julia,
>>
>> this is a Java VM argument that you need to set in the Eclipse Run
>> (or Debug) Configuration for your main class. I suppose you did not
>> set this in the correct place. See schreenshot from below.
>>
>> And, one more important thing: You cannot set a bigger heap size than
>> the size of your physical memory. Please read this for more details:
>> http://protege.cim3.net/cgi-bin/wiki.pl?ScalabilityAndTuning
>>
>> Try to set the heap size to 250M ("-Xmx250M").
>>
>> Tania
>>
>>
>>
>>
>> Nikolaj Berntsen wrote:
>>
>>> Julia Dmitrieva wrote:
>>>
>>>  
>>>
>>>> Hello Nikolai,
>>>>
>>>> I have tryed it, the problem is just the same:
>>>> thus I still have:
>>>> CONFIG: Protege 3.2 Build 300, JVM 1.5.0_06-b05, memory=66M, Windows
>>>> 2000, encoding=UTF-8, language=en, country=US
>>>>
>>>> May be I am not understanding something important,
>>>>  
>>>
>>>
>>>
>>> my guess is that you don't set the options the right place. I have not
>>> tried to pass parameters to protege, so I cannot help you out with
>>> this one.
>>>
>>> Good luck,
>>> /\/
>>>
>>>
>>>  
>>>
>>
>> -------------------------------------------------------------------------
>>
>> To unsubscribe go to
>> http://protege.stanford.edu/community/subscribe.html
>
>
>
>
> ------------------------------------------------------------------------
>

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