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Posted to user@ctakes.apache.org by Joshua Weiner <jo...@gmail.com> on 2013/12/22 01:11:52 UTC
Help running AggregatePlaintextProcessor
Hello everyone,
I am trying to use cTAKES (just downloaded it) and when trying to load the
analysis engine AE *AggregatePlaintextProcessor* (per this link:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide#cTAKES3.1UserInstallGuide-Prerequisites
)
I get this error:
Loading model:
................................
scope model:
/C:/apache-ctakes-3.1.0/resources/org/apache/ctakes/assertion/models/scope.model
Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC
overhead limit exceeded
I am on Windows 8, 8gb of ram. It appears that other AE work.. but I know
AggregatePlaintextProcessor is the most important one.
Thank you so much for any help! This is very important to me. Please feel
free to respond to me directly at my email address: joshuaweiner2@gmail.com
Josh
--
Joshua S. Weiner
joshuaweiner2@gmail.com
201.638.0047
Re: Help running AggregatePlaintextProcessor
Posted by Pan Teng <te...@udel.edu>.
Hi Josh,
I tried to increased the heap size by editing both the runctakesCVD.sh file and runctakesCPE.sh file. For you maybe you can try the bat file for windows? Hope this will work for you too. Happy holiday everyone! \^_^/
Pan
> On Dec 22, 2013, at 6:44 AM, Joshua Weiner <jo...@gmail.com> wrote:
>
> Hi Paula,
>
> Thank you SO much for your response. I have been literally trying to fix this for 5+ hours. I don't have permissions to use the ULMS version yet so I am trying to make this work. Unfortunately I am not using eclipse so his method for increasing does not make sense. Can you expand? Were you in eclipse? Previously, i googled how to increase Heapsize, and changed settings in my java application. If I go to configure Java Control Panel I added the following runtime parameter:
> -Xmx2048m for both user and system... to no avail.
>
> I sincerely appreciate your help. Are you telling me that when I get the ULMS version it won't use as much memory?
>
> THanks,
> Josh
>
>
>
>
>> On Sun, Dec 22, 2013 at 2:36 AM, digital paula <cy...@hotmail.com> wrote:
>> Hi Josh,
>>
>> Yes, I had the same problem but my friend Samir helped me out. :-) You have to increase your JRE memory. Please see my post and Samir's from October, I think it was early October.
>>
>> Actually the ULMS version of the AggregatePlaintextProcessor is more important.
>>
>> Regards,
>> Paula
>>
>> From: joshuaweiner2@gmail.com
>> Date: Sat, 21 Dec 2013 19:11:52 -0500
>> Subject: Help running AggregatePlaintextProcessor
>> To: user@ctakes.apache.org
>>
>>
>> Hello everyone,
>>
>> I am trying to use cTAKES (just downloaded it) and when trying to load the analysis engine AE AggregatePlaintextProcessor (per this link: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide#cTAKES3.1UserInstallGuide-Prerequisites)
>>
>> I get this error:
>> Loading model:
>> ................................
>> scope model: /C:/apache-ctakes-3.1.0/resources/org/apache/ctakes/assertion/models/scope.model
>> Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
>>
>> I am on Windows 8, 8gb of ram. It appears that other AE work.. but I know AggregatePlaintextProcessor is the most important one.
>>
>> Thank you so much for any help! This is very important to me. Please feel free to respond to me directly at my email address: joshuaweiner2@gmail.com
>>
>> Josh
>>
>>
>>
>> --
>> Joshua S. Weiner
>> joshuaweiner2@gmail.com
>> 201.638.0047
>
>
>
> --
> Joshua S. Weiner
> joshuaweiner2@gmail.com
> 201.638.0047
Re: Help running AggregatePlaintextProcessor
Posted by Joshua Weiner <jo...@gmail.com>.
Ironically enough, it just started working. Let me wait until I get the
ULMS license privelledges and then see if it works. Thank you so much for
all of your help guys.Very welcoming community - glad to be a member. If
anyone needs statistics or machine learning help let me know!
Josh
On Sun, Dec 22, 2013 at 9:04 PM, Karthik Sarma <ks...@ksarma.com> wrote:
> Josh, you should be able to add -Xms500m -Xmx4000m to the command line
> arguments in the run scripts in order to increase the heap size available
> for your JRE. If that doesn't work, it is likely something else is wrong.
> If you could post in more detail what exactly you are trying to do, that
> would be helpful
>
>
>
>
>
> --
> Karthik Sarma
> UCLA Medical Scientist Training Program Class of 20??
> Member, UCLA Medical Imaging & Informatics Lab
> Member, CA Delegation to the House of Delegates of the American Medical
> Association
> ksarma@ksarma.com
> gchat: ksarma@gmail.com
> linkedin: www.linkedin.com/in/ksarma
>
>
> On Sun, Dec 22, 2013 at 5:26 PM, digital paula <cy...@hotmail.com>wrote:
>
>> Josh,
>>
>> ULMS also uses a lot of memory especially since it contains the full
>> vocabulary for annotating in terms of recognizing diseases, anatomy, meds,
>> etc. Though, to get the plaintext processor (without ULMS) still requires
>> a lot of memory because of all the components it calls just like the
>> aggregate processor using ULMS.
>>
>> I'm using Eclipse but do try what the other folks recommended but if for
>> whatever reason nothing works use this as a last resort. Gamers do this to
>> increase their memory for JRE. Create an environmental variable(1st line
>> below) with value(2nd line below) :
>>
>> _JAVA_OPTIONS
>>
>> -Xms500m -Xmx4000m
>>
>> Regards,
>> Paula
>>
>> ------------------------------
>> From: joshuaweiner2@gmail.com
>> Date: Sun, 22 Dec 2013 06:44:04 -0500
>> Subject: Re: Help running AggregatePlaintextProcessor
>>
>> To: user@ctakes.apache.org
>>
>> Hi Paula,
>>
>> Thank you SO much for your response. I have been literally trying to fix
>> this for 5+ hours. I don't have permissions to use the ULMS version yet so
>> I am trying to make this work. Unfortunately I am not using eclipse so his
>> method for increasing does not make sense. Can you expand? Were you in
>> eclipse? Previously, i googled how to increase Heapsize, and changed
>> settings in my java application. If I go to configure Java Control Panel I
>> added the following runtime parameter:
>> -Xmx2048m for both user and system... to no avail.
>>
>> I sincerely appreciate your help. Are you telling me that when I get the
>> ULMS version it won't use as much memory?
>>
>> THanks,
>> Josh
>>
>>
>>
>>
>> On Sun, Dec 22, 2013 at 2:36 AM, digital paula <cy...@hotmail.com>wrote:
>>
>> Hi Josh,
>>
>> Yes, I had the same problem but my friend Samir helped me out. :-) You
>> have to increase your JRE memory. Please see my post and Samir's from
>> October, I think it was early October.
>>
>> Actually the ULMS version of the AggregatePlaintextProcessor is more
>> important.
>>
>> Regards,
>> Paula
>>
>> ------------------------------
>> From: joshuaweiner2@gmail.com
>> Date: Sat, 21 Dec 2013 19:11:52 -0500
>> Subject: Help running AggregatePlaintextProcessor
>> To: user@ctakes.apache.org
>>
>>
>> Hello everyone,
>>
>> I am trying to use cTAKES (just downloaded it) and when trying to load
>> the analysis engine AE *AggregatePlaintextProcessor* (per this link:
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide#cTAKES3.1UserInstallGuide-Prerequisites
>> )
>>
>> I get this error:
>> Loading model:
>> ................................
>> scope model:
>> /C:/apache-ctakes-3.1.0/resources/org/apache/ctakes/assertion/models/scope.model
>> Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC
>> overhead limit exceeded
>>
>> I am on Windows 8, 8gb of ram. It appears that other AE work.. but I know
>> AggregatePlaintextProcessor is the most important one.
>>
>> Thank you so much for any help! This is very important to me. Please
>> feel free to respond to me directly at my email address:
>> joshuaweiner2@gmail.com
>>
>> Josh
>>
>>
>>
>> --
>> Joshua S. Weiner
>> joshuaweiner2@gmail.com
>> 201.638.0047
>>
>>
>>
>>
>> --
>> Joshua S. Weiner
>> joshuaweiner2@gmail.com
>> 201.638.0047
>>
>
>
--
Joshua S. Weiner
joshuaweiner2@gmail.com
201.638.0047
Re: Help running AggregatePlaintextProcessor
Posted by Karthik Sarma <ks...@ksarma.com>.
Josh, you should be able to add -Xms500m -Xmx4000m to the command line
arguments in the run scripts in order to increase the heap size available
for your JRE. If that doesn't work, it is likely something else is wrong.
If you could post in more detail what exactly you are trying to do, that
would be helpful
--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical
Association
ksarma@ksarma.com
gchat: ksarma@gmail.com
linkedin: www.linkedin.com/in/ksarma
On Sun, Dec 22, 2013 at 5:26 PM, digital paula <cy...@hotmail.com>wrote:
> Josh,
>
> ULMS also uses a lot of memory especially since it contains the full
> vocabulary for annotating in terms of recognizing diseases, anatomy, meds,
> etc. Though, to get the plaintext processor (without ULMS) still requires
> a lot of memory because of all the components it calls just like the
> aggregate processor using ULMS.
>
> I'm using Eclipse but do try what the other folks recommended but if for
> whatever reason nothing works use this as a last resort. Gamers do this to
> increase their memory for JRE. Create an environmental variable(1st line
> below) with value(2nd line below) :
>
> _JAVA_OPTIONS
>
> -Xms500m -Xmx4000m
>
> Regards,
> Paula
>
> ------------------------------
> From: joshuaweiner2@gmail.com
> Date: Sun, 22 Dec 2013 06:44:04 -0500
> Subject: Re: Help running AggregatePlaintextProcessor
>
> To: user@ctakes.apache.org
>
> Hi Paula,
>
> Thank you SO much for your response. I have been literally trying to fix
> this for 5+ hours. I don't have permissions to use the ULMS version yet so
> I am trying to make this work. Unfortunately I am not using eclipse so his
> method for increasing does not make sense. Can you expand? Were you in
> eclipse? Previously, i googled how to increase Heapsize, and changed
> settings in my java application. If I go to configure Java Control Panel I
> added the following runtime parameter:
> -Xmx2048m for both user and system... to no avail.
>
> I sincerely appreciate your help. Are you telling me that when I get the
> ULMS version it won't use as much memory?
>
> THanks,
> Josh
>
>
>
>
> On Sun, Dec 22, 2013 at 2:36 AM, digital paula <cy...@hotmail.com>wrote:
>
> Hi Josh,
>
> Yes, I had the same problem but my friend Samir helped me out. :-) You
> have to increase your JRE memory. Please see my post and Samir's from
> October, I think it was early October.
>
> Actually the ULMS version of the AggregatePlaintextProcessor is more
> important.
>
> Regards,
> Paula
>
> ------------------------------
> From: joshuaweiner2@gmail.com
> Date: Sat, 21 Dec 2013 19:11:52 -0500
> Subject: Help running AggregatePlaintextProcessor
> To: user@ctakes.apache.org
>
>
> Hello everyone,
>
> I am trying to use cTAKES (just downloaded it) and when trying to load the
> analysis engine AE *AggregatePlaintextProcessor* (per this link:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide#cTAKES3.1UserInstallGuide-Prerequisites
> )
>
> I get this error:
> Loading model:
> ................................
> scope model:
> /C:/apache-ctakes-3.1.0/resources/org/apache/ctakes/assertion/models/scope.model
> Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC
> overhead limit exceeded
>
> I am on Windows 8, 8gb of ram. It appears that other AE work.. but I know
> AggregatePlaintextProcessor is the most important one.
>
> Thank you so much for any help! This is very important to me. Please feel
> free to respond to me directly at my email address:
> joshuaweiner2@gmail.com
>
> Josh
>
>
>
> --
> Joshua S. Weiner
> joshuaweiner2@gmail.com
> 201.638.0047
>
>
>
>
> --
> Joshua S. Weiner
> joshuaweiner2@gmail.com
> 201.638.0047
>
RE: Help running AggregatePlaintextProcessor
Posted by digital paula <cy...@hotmail.com>.
Josh,
ULMS also uses a lot of memory especially since it contains the full vocabulary for annotating in terms of recognizing diseases, anatomy, meds, etc. Though, to get the plaintext processor (without ULMS) still requires a lot of memory because of all the components it calls just like the aggregate processor using ULMS.
I'm using Eclipse but do try what the other folks recommended but if for whatever reason nothing works use this as a last resort. Gamers do this to increase their memory for JRE. Create an environmental variable(1st line below) with value(2nd line below) :
_JAVA_OPTIONS
-Xms500m -Xmx4000m
Regards,
Paula
From: joshuaweiner2@gmail.com
Date: Sun, 22 Dec 2013 06:44:04 -0500
Subject: Re: Help running AggregatePlaintextProcessor
To: user@ctakes.apache.org
Hi Paula,
Thank you SO much for your response. I have been literally trying to fix this for 5+ hours. I don't have permissions to use the ULMS version yet so I am trying to make this work. Unfortunately I am not using eclipse so his method for increasing does not make sense. Can you expand? Were you in eclipse? Previously, i googled how to increase Heapsize, and changed settings in my java application. If I go to configure Java Control Panel I added the following runtime parameter:
-Xmx2048m for both user and system... to no avail.
I sincerely appreciate your help. Are you telling me that when I get the ULMS version it won't use as much memory?
THanks,
Josh
On Sun, Dec 22, 2013 at 2:36 AM, digital paula <cy...@hotmail.com> wrote:
Hi Josh,
Yes, I had the same problem but my friend Samir helped me out. :-) You have to increase your JRE memory. Please see my post and Samir's from October, I think it was early October.
Actually the ULMS version of the AggregatePlaintextProcessor is more important.
Regards,
Paula
From: joshuaweiner2@gmail.com
Date: Sat, 21 Dec 2013 19:11:52 -0500
Subject: Help running AggregatePlaintextProcessor
To: user@ctakes.apache.org
Hello everyone,
I am trying to use cTAKES (just downloaded it) and when trying to load the analysis engine AE AggregatePlaintextProcessor (per this link: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide#cTAKES3.1UserInstallGuide-Prerequisites)
I get this error:Loading model:................................scope model: /C:/apache-ctakes-3.1.0/resources/org/apache/ctakes/assertion/models/scope.modelException in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
I am on Windows 8, 8gb of ram. It appears that other AE work.. but I know AggregatePlaintextProcessor is the most important one.
Thank you so much for any help! This is very important to me. Please feel free to respond to me directly at my email address: joshuaweiner2@gmail.com
Josh
--
Joshua S. Weiner
joshuaweiner2@gmail.com
201.638.0047
--
Joshua S. Weiner
joshuaweiner2@gmail.com201.638.0047
Re: Help running AggregatePlaintextProcessor
Posted by Joshua Weiner <jo...@gmail.com>.
Hi Paula,
Thank you SO much for your response. I have been literally trying to fix
this for 5+ hours. I don't have permissions to use the ULMS version yet so
I am trying to make this work. Unfortunately I am not using eclipse so his
method for increasing does not make sense. Can you expand? Were you in
eclipse? Previously, i googled how to increase Heapsize, and changed
settings in my java application. If I go to configure Java Control Panel I
added the following runtime parameter:
-Xmx2048m for both user and system... to no avail.
I sincerely appreciate your help. Are you telling me that when I get the
ULMS version it won't use as much memory?
THanks,
Josh
On Sun, Dec 22, 2013 at 2:36 AM, digital paula <cy...@hotmail.com>wrote:
> Hi Josh,
>
> Yes, I had the same problem but my friend Samir helped me out. :-) You
> have to increase your JRE memory. Please see my post and Samir's from
> October, I think it was early October.
>
> Actually the ULMS version of the AggregatePlaintextProcessor is more
> important.
>
> Regards,
> Paula
>
> ------------------------------
> From: joshuaweiner2@gmail.com
> Date: Sat, 21 Dec 2013 19:11:52 -0500
> Subject: Help running AggregatePlaintextProcessor
> To: user@ctakes.apache.org
>
>
> Hello everyone,
>
> I am trying to use cTAKES (just downloaded it) and when trying to load the
> analysis engine AE *AggregatePlaintextProcessor* (per this link:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide#cTAKES3.1UserInstallGuide-Prerequisites
> )
>
> I get this error:
> Loading model:
> ................................
> scope model:
> /C:/apache-ctakes-3.1.0/resources/org/apache/ctakes/assertion/models/scope.model
> Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC
> overhead limit exceeded
>
> I am on Windows 8, 8gb of ram. It appears that other AE work.. but I know
> AggregatePlaintextProcessor is the most important one.
>
> Thank you so much for any help! This is very important to me. Please feel
> free to respond to me directly at my email address:
> joshuaweiner2@gmail.com
>
> Josh
>
>
>
> --
> Joshua S. Weiner
> joshuaweiner2@gmail.com
> 201.638.0047
>
--
Joshua S. Weiner
joshuaweiner2@gmail.com
201.638.0047
RE: Help running AggregatePlaintextProcessor
Posted by digital paula <cy...@hotmail.com>.
Hi Josh,
Yes, I had the same problem but my friend Samir helped me out. :-) You have to increase your JRE memory. Please see my post and Samir's from October, I think it was early October.
Actually the ULMS version of the AggregatePlaintextProcessor is more important.
Regards,
Paula
From: joshuaweiner2@gmail.com
Date: Sat, 21 Dec 2013 19:11:52 -0500
Subject: Help running AggregatePlaintextProcessor
To: user@ctakes.apache.org
Hello everyone,
I am trying to use cTAKES (just downloaded it) and when trying to load the analysis engine AE AggregatePlaintextProcessor (per this link: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide#cTAKES3.1UserInstallGuide-Prerequisites)
I get this error:Loading model:................................scope model: /C:/apache-ctakes-3.1.0/resources/org/apache/ctakes/assertion/models/scope.modelException in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
I am on Windows 8, 8gb of ram. It appears that other AE work.. but I know AggregatePlaintextProcessor is the most important one.
Thank you so much for any help! This is very important to me. Please feel free to respond to me directly at my email address: joshuaweiner2@gmail.com
Josh
--
Joshua S. Weiner
joshuaweiner2@gmail.com
201.638.0047