Problems loading SNOMED CT into Protege

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Problems loading SNOMED CT into Protege

Campbell, James R

I am trying to open SNOMED CT which I received from Harold Solbrig on my Windows 7 64 bit machine with 16GB memory.  Scott Campbell guided me to increase my JAVA memory  to 4min-8maxGB before we tried.  We verified the file was a valid OWL file on his MAC.  I am getting this memory error

 

java.lag.OutOfMemoryError:  GC overhead limit exceeded

 

which alternated with a hash stack error.  We thought that editing the parameter for JAVA memory was supposed to deal with this issue but I must be doing something wrong. 

 

Suggestions?

Jim Campbell


The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
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Re: Problems loading SNOMED CT into Protege

Matthew Horridge-2
Administrator
Hi Jim,

When you use Scott’s machine, is it possible to load SNOMED?  

A few more questions,

(1) Please can you post your exact settings to the list so that I can double check them?

(2) Which version of Protege are you running?

(3) Are you able to share a copy of the ontology with me (somehow)?

Cheers,

Matthew

On 24 Nov 2014, at 11:17, Campbell, James R <[hidden email]> wrote:

I am trying to open SNOMED CT which I received from Harold Solbrig on my Windows 7 64 bit machine with 16GB memory.  Scott Campbell guided me to increase my JAVA memory  to 4min-8maxGB before we tried.  We verified the file was a valid OWL file on his MAC.  I am getting this memory error

 

java.lag.OutOfMemoryError:  GC overhead limit exceeded

 

which alternated with a hash stack error.  We thought that editing the parameter for JAVA memory was supposed to deal with this issue but I must be doing something wrong. 

 

Suggestions?
Jim Campbell

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
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Re: Problems loading SNOMED CT into Protege

samsontu
In reply to this post by Campbell, James R
Hi Jim,

When you run Protege on Windows, you should a black console window that display a  trace of Protege’s activities. Near the top of the console window, you should see something like:

Starting Protege Desktop (Version 5.0.0, Build = beta-15)
Platform:
    Java: JVM 1.7.0_67-b01 Memory: 2330M
    Language: en, Country: US
    Framework: Apache Software Foundation (1.5)
    OS: macos (10.10.1)
    Processor: x86-64

It would be good if you can send us this information. With 2330M of memory, I have no problem loading into Protege the 20140731 version of SNOMED CT OWL ontology that I generated from the NLM distribution. 

The 3.x version of Protege is much less efficient in memory management. I’d recommend that you use the 5.0 beta.

With best regards,
Samson


On Nov 24, 2014, at 11:17 AM, Campbell, James R <[hidden email]> wrote:

I am trying to open SNOMED CT which I received from Harold Solbrig on my Windows 7 64 bit machine with 16GB memory.  Scott Campbell guided me to increase my JAVA memory  to 4min-8maxGB before we tried.  We verified the file was a valid OWL file on his MAC.  I am getting this memory error

 

java.lag.OutOfMemoryError:  GC overhead limit exceeded

 

which alternated with a hash stack error.  We thought that editing the parameter for JAVA memory was supposed to deal with this issue but I must be doing something wrong. 

 

Suggestions?
Jim Campbell

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Problems loading SNOMED CT into Protege

Campbell, James R

I have enclosed the console message at startup Samson.  I am currently on 4.3 Protégé and am always a bit reluctant to use a beta.  I reinstalled this morning as one effort a correction.  Will here be material benefit over 4.3 of installing 5 (and no headaches?)

Jim


From: protege-user [[hidden email]] on behalf of Samson Tu [[hidden email]]
Sent: Monday, November 24, 2014 1:48 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Problems loading SNOMED CT into Protege

Hi Jim,

When you run Protege on Windows, you should a black console window that display a  trace of Protege’s activities. Near the top of the console window, you should see something like:

Starting Protege Desktop (Version 5.0.0, Build = beta-15)
Platform:
    Java: JVM 1.7.0_67-b01 Memory: 2330M
    Language: en, Country: US
    Framework: Apache Software Foundation (1.5)
    OS: macos (10.10.1)
    Processor: x86-64

It would be good if you can send us this information. With 2330M of memory, I have no problem loading into Protege the 20140731 version of SNOMED CT OWL ontology that I generated from the NLM distribution. 

The 3.x version of Protege is much less efficient in memory management. I’d recommend that you use the 5.0 beta.

With best regards,
Samson


On Nov 24, 2014, at 11:17 AM, Campbell, James R <[hidden email]> wrote:

I am trying to open SNOMED CT which I received from Harold Solbrig on my Windows 7 64 bit machine with 16GB memory.  Scott Campbell guided me to increase my JAVA memory  to 4min-8maxGB before we tried.  We verified the file was a valid OWL file on his MAC.  I am getting this memory error

 

java.lag.OutOfMemoryError:  GC overhead limit exceeded

 

which alternated with a hash stack error.  We thought that editing the parameter for JAVA memory was supposed to deal with this issue but I must be doing something wrong. 

 

Suggestions?
Jim Campbell

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Problems loading SNOMED CT into Protege

rhausam
Jim,

I don't see an error in the file that you attached, but it does show that Java is being allocated only 466M of RAM, which definitely isn't enough to load all of SNOMED CT.  You may be launching Java and Protege via LAX, which unfortunately limits the maximum amount of RAM available to the JVM (but I didn't think the LAX limit was actually quite that small), or maybe there's an error in your memory parameter(s).  To get around the LAX limitation I've instead launched via run.bat (for Windows, or run.sh for Linux).  Also, I've found that it's been necessary to increase the Java stack space by setting the -Xss option (I've typically used a value of -Xss2M).  You should have plenty of RAM, once Java is able to make use of it.

The run.bat command that I've typically used has looked something like:

...\java.exe -server -Xmx10G -Xss2M -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/felix.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher

Rob

On Mon, Nov 24, 2014 at 3:26 PM, Campbell, James R <[hidden email]> wrote:

I have enclosed the console message at startup Samson.  I am currently on 4.3 Protégé and am always a bit reluctant to use a beta.  I reinstalled this morning as one effort a correction.  Will here be material benefit over 4.3 of installing 5 (and no headaches?)

Jim


From: protege-user [[hidden email]] on behalf of Samson Tu [[hidden email]]
Sent: Monday, November 24, 2014 1:48 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Problems loading SNOMED CT into Protege

Hi Jim,

When you run Protege on Windows, you should a black console window that display a  trace of Protege’s activities. Near the top of the console window, you should see something like:

Starting Protege Desktop (Version 5.0.0, Build = beta-15)
Platform:
    Java: JVM 1.7.0_67-b01 Memory: 2330M
    Language: en, Country: US
    Framework: Apache Software Foundation (1.5)
    OS: macos (10.10.1)
    Processor: x86-64

It would be good if you can send us this information. With 2330M of memory, I have no problem loading into Protege the 20140731 version of SNOMED CT OWL ontology that I generated from the NLM distribution. 

The 3.x version of Protege is much less efficient in memory management. I’d recommend that you use the 5.0 beta.

With best regards,
Samson


On Nov 24, 2014, at 11:17 AM, Campbell, James R <[hidden email]> wrote:

I am trying to open SNOMED CT which I received from Harold Solbrig on my Windows 7 64 bit machine with 16GB memory.  Scott Campbell guided me to increase my JAVA memory  to 4min-8maxGB before we tried.  We verified the file was a valid OWL file on his MAC.  I am getting this memory error

 

java.lag.OutOfMemoryError:  GC overhead limit exceeded

 

which alternated with a hash stack error.  We thought that editing the parameter for JAVA memory was supposed to deal with this issue but I must be doing something wrong. 

 

Suggestions?
Jim Campbell

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user




--
Robert Hausam, MD
Hausam Consulting LLC
<a href="tel:%2B1%20%28801%29%20949-1556" value="+18019491556" target="_blank">+1 (801) 949-1556


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Re: Problems loading SNOMED CT into Protege

Campbell, James R

Sorry, I thought that Samson was requesting the top of the stack...here is the rest

Jim


From: protege-user [[hidden email]] on behalf of Robert Hausam [[hidden email]]
Sent: Monday, November 24, 2014 6:43 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Problems loading SNOMED CT into Protege

Jim,

I don't see an error in the file that you attached, but it does show that Java is being allocated only 466M of RAM, which definitely isn't enough to load all of SNOMED CT.  You may be launching Java and Protege via LAX, which unfortunately limits the maximum amount of RAM available to the JVM (but I didn't think the LAX limit was actually quite that small), or maybe there's an error in your memory parameter(s).  To get around the LAX limitation I've instead launched via run.bat (for Windows, or run.sh for Linux).  Also, I've found that it's been necessary to increase the Java stack space by setting the -Xss option (I've typically used a value of -Xss2M).  You should have plenty of RAM, once Java is able to make use of it.

The run.bat command that I've typically used has looked something like:

...\java.exe -server -Xmx10G -Xss2M -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bin/felix.jar;bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher

Rob

On Mon, Nov 24, 2014 at 3:26 PM, Campbell, James R <[hidden email]> wrote:

I have enclosed the console message at startup Samson.  I am currently on 4.3 Protégé and am always a bit reluctant to use a beta.  I reinstalled this morning as one effort a correction.  Will here be material benefit over 4.3 of installing 5 (and no headaches?)

Jim


From: protege-user [[hidden email]] on behalf of Samson Tu [[hidden email]]
Sent: Monday, November 24, 2014 1:48 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Problems loading SNOMED CT into Protege

Hi Jim,

When you run Protege on Windows, you should a black console window that display a  trace of Protege’s activities. Near the top of the console window, you should see something like:

Starting Protege Desktop (Version 5.0.0, Build = beta-15)
Platform:
    Java: JVM 1.7.0_67-b01 Memory: 2330M
    Language: en, Country: US
    Framework: Apache Software Foundation (1.5)
    OS: macos (10.10.1)
    Processor: x86-64

It would be good if you can send us this information. With 2330M of memory, I have no problem loading into Protege the 20140731 version of SNOMED CT OWL ontology that I generated from the NLM distribution. 

The 3.x version of Protege is much less efficient in memory management. I’d recommend that you use the 5.0 beta.

With best regards,
Samson


On Nov 24, 2014, at 11:17 AM, Campbell, James R <[hidden email]> wrote:

I am trying to open SNOMED CT which I received from Harold Solbrig on my Windows 7 64 bit machine with 16GB memory.  Scott Campbell guided me to increase my JAVA memory  to 4min-8maxGB before we tried.  We verified the file was a valid OWL file on his MAC.  I am getting this memory error

 

java.lag.OutOfMemoryError:  GC overhead limit exceeded

 

which alternated with a hash stack error.  We thought that editing the parameter for JAVA memory was supposed to deal with this issue but I must be doing something wrong. 

 

Suggestions?
Jim Campbell

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user




--
Robert Hausam, MD
Hausam Consulting LLC
<a href="tel:%2B1%20%28801%29%20949-1556" target="_blank" value="&#43;18019491556">+1 (801) 949-1556


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Problems loading SNOMED CT into Protege

samsontu
In reply to this post by Campbell, James R
Hi Jim,

Using Protege 4.3 is fine. 

Your screen dump shows that you were starting the Java VM with -Xms262,144,000 -Xmx524,288,000 (commas added). That means a maximum of 524 MB. That’s not enough for loading SNOMED CT.

As Robert suggested, you can edit and run the “run.bat” file to set the -XMx parameter (e.g., -XM4G). On my Mac, my Protege instance starts with 2330M of memory, and that’s enough for loading SNOMED CT.

With best regards,
Samson



On Nov 24, 2014, at 2:26 PM, Campbell, James R <[hidden email]> wrote:

I have enclosed the console message at startup Samson.  I am currently on 4.3 Protégé and am always a bit reluctant to use a beta.  I reinstalled this morning as one effort a correction.  Will here be material benefit over 4.3 of installing 5 (and no headaches?)
Jim

From: protege-user [[hidden email]] on behalf of Samson Tu [[hidden email]]
Sent: Monday, November 24, 2014 1:48 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Problems loading SNOMED CT into Protege

Hi Jim,

When you run Protege on Windows, you should a black console window that display a  trace of Protege’s activities. Near the top of the console window, you should see something like:

Starting Protege Desktop (Version 5.0.0, Build = beta-15)
Platform:
    Java: JVM 1.7.0_67-b01 Memory: 2330M
    Language: en, Country: US
    Framework: Apache Software Foundation (1.5)
    OS: macos (10.10.1)
    Processor: x86-64

It would be good if you can send us this information. With 2330M of memory, I have no problem loading into Protege the 20140731 version of SNOMED CT OWL ontology that I generated from the NLM distribution. 

The 3.x version of Protege is much less efficient in memory management. I’d recommend that you use the 5.0 beta.

With best regards,
Samson


On Nov 24, 2014, at 11:17 AM, Campbell, James R <[hidden email]> wrote:

I am trying to open SNOMED CT which I received from Harold Solbrig on my Windows 7 64 bit machine with 16GB memory.  Scott Campbell guided me to increase my JAVA memory  to 4min-8maxGB before we tried.  We verified the file was a valid OWL file on his MAC.  I am getting this memory error

 

java.lag.OutOfMemoryError:  GC overhead limit exceeded

 

which alternated with a hash stack error.  We thought that editing the parameter for JAVA memory was supposed to deal with this issue but I must be doing something wrong. 

 

Suggestions?
Jim Campbell

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

<Errors.docx>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
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[hidden email]
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Re: Problems loading SNOMED CT into Protege

rhausam
Yes, that should do it.

Rob

On Mon, Nov 24, 2014 at 6:36 PM, Samson Tu <[hidden email]> wrote:
Hi Jim,

Using Protege 4.3 is fine. 

Your screen dump shows that you were starting the Java VM with -Xms262,144,000 -Xmx524,288,000 (commas added). That means a maximum of 524 MB. That’s not enough for loading SNOMED CT.

As Robert suggested, you can edit and run the “run.bat” file to set the -XMx parameter (e.g., -XM4G). On my Mac, my Protege instance starts with 2330M of memory, and that’s enough for loading SNOMED CT.

With best regards,
Samson



On Nov 24, 2014, at 2:26 PM, Campbell, James R <[hidden email]> wrote:

I have enclosed the console message at startup Samson.  I am currently on 4.3 Protégé and am always a bit reluctant to use a beta.  I reinstalled this morning as one effort a correction.  Will here be material benefit over 4.3 of installing 5 (and no headaches?)
Jim

From: protege-user [[hidden email]] on behalf of Samson Tu [[hidden email]]
Sent: Monday, November 24, 2014 1:48 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Problems loading SNOMED CT into Protege

Hi Jim,

When you run Protege on Windows, you should a black console window that display a  trace of Protege’s activities. Near the top of the console window, you should see something like:

Starting Protege Desktop (Version 5.0.0, Build = beta-15)
Platform:
    Java: JVM 1.7.0_67-b01 Memory: 2330M
    Language: en, Country: US
    Framework: Apache Software Foundation (1.5)
    OS: macos (10.10.1)
    Processor: x86-64

It would be good if you can send us this information. With 2330M of memory, I have no problem loading into Protege the 20140731 version of SNOMED CT OWL ontology that I generated from the NLM distribution. 

The 3.x version of Protege is much less efficient in memory management. I’d recommend that you use the 5.0 beta.

With best regards,
Samson


On Nov 24, 2014, at 11:17 AM, Campbell, James R <[hidden email]> wrote:

I am trying to open SNOMED CT which I received from Harold Solbrig on my Windows 7 64 bit machine with 16GB memory.  Scott Campbell guided me to increase my JAVA memory  to 4min-8maxGB before we tried.  We verified the file was a valid OWL file on his MAC.  I am getting this memory error

 

java.lag.OutOfMemoryError:  GC overhead limit exceeded

 

which alternated with a hash stack error.  We thought that editing the parameter for JAVA memory was supposed to deal with this issue but I must be doing something wrong. 

 

Suggestions?
Jim Campbell

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

<Errors.docx>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user




--
Robert Hausam, MD
Hausam Consulting LLC
+1 (801) 949-1556


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user