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Posted to dev@ctakes.apache.org by "Finan, Sean" <Se...@childrens.harvard.edu> on 2019/01/11 15:15:15 UTC
Re: Not able to run cTAKES UMLS in parallel [EXTERNAL]
Hi Kalyani,
At a guess, each parallel instance of ctakes is attempting to write some log file concurrently and the system does not approve.
Have other people out there witnessed and overcome this problem?
Sean
________________________________________
From: Kalyani Unnikrishnan <ka...@hilabs.com>
Sent: Friday, January 11, 2019 5:15 AM
To: dev@ctakes.apache.org
Subject: Not able to run cTAKES UMLS in parallel [EXTERNAL]
Hi,
I am trying to make cTAKES accessible by multiple programs in parallel. I was able to remove the error on umls.lck by setting PARAMS_ISOLATION to TRANSACTION_SERIALIZABLE. But I am still getting the following error when multiple programs are running the pipeline at the same time (it works fine if it is run in sequence).
Caused by: java.sql.SQLException: file input/output error: org/apache/ctakes/dictionary/lookup/umls2011ab/umls.log
at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source)
at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source)
at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:247)
at org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:109)
... 47 more
Caused by: org.hsqldb.HsqlException: file input/output error: org/apache/ctakes/dictionary/lookup/umls2011ab/umls.log
at org.hsqldb.error.Error.error(Unknown Source)
at org.hsqldb.error.Error.error(Unknown Source)
at org.hsqldb.persist.Log.openLog(Unknown Source)
at org.hsqldb.persist.Log.open(Unknown Source)
at org.hsqldb.persist.Logger.open(Unknown Source)
at org.hsqldb.Database.reopen(Unknown Source)
at org.hsqldb.Database.open(Unknown Source)
at org.hsqldb.DatabaseManager.getDatabase(Unknown Source)
at org.hsqldb.DatabaseManager.newSession(Unknown Source)
... 53 more
Appreciate any inputs.
Regards,
Kalyani
Re: Not able to run cTAKES UMLS in parallel [EXTERNAL]
Posted by gandhi rajan <ga...@gmail.com>.
Completely agree. Kalyani, you could give it a try testing with MySQL DB.
On Friday, January 11, 2019, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Most likely. That is the old dictionary lookup, which keeps open access
> to a file database.
> ________________________________________
> From: gandhi rajan <ga...@gmail.com>
> Sent: Friday, January 11, 2019 12:39 PM
> To: dev@ctakes.apache.org
> Subject: Re: Not able to run cTAKES UMLS in parallel [EXTERNAL]
>
> Hi, Have faced issues related to connectivity timeout using mysql db. But
> never faced concurrency issue in our testing. Is it hsql db specific by any
> chance?
>
> On Friday, January 11, 2019, Finan, Sean <Sean.Finan@childrens.harvard.edu
> >
> wrote:
>
> > Hi Kalyani,
> >
> > At a guess, each parallel instance of ctakes is attempting to write some
> > log file concurrently and the system does not approve.
> >
> > Have other people out there witnessed and overcome this problem?
> >
> > Sean
> > ________________________________________
> > From: Kalyani Unnikrishnan <ka...@hilabs.com>
> > Sent: Friday, January 11, 2019 5:15 AM
> > To: dev@ctakes.apache.org
> > Subject: Not able to run cTAKES UMLS in parallel [EXTERNAL]
> >
> > Hi,
> >
> > I am trying to make cTAKES accessible by multiple programs in parallel. I
> > was able to remove the error on umls.lck by setting PARAMS_ISOLATION to
> > TRANSACTION_SERIALIZABLE. But I am still getting the following error when
> > multiple programs are running the pipeline at the same time (it works
> fine
> > if it is run in sequence).
> >
> > Caused by: java.sql.SQLException: file input/output error:
> > org/apache/ctakes/dictionary/lookup/umls2011ab/umls.log
> > at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
> > at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
> > at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source)
> > at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source)
> > at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source)
> > at java.sql.DriverManager.getConnection(DriverManager.java:664)
> > at java.sql.DriverManager.getConnection(DriverManager.java:247)
> > at org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.
> > load(JdbcConnectionResourceImpl.java:109)
> > ... 47 more
> > Caused by: org.hsqldb.HsqlException: file input/output error:
> > org/apache/ctakes/dictionary/lookup/umls2011ab/umls.log
> > at org.hsqldb.error.Error.error(Unknown Source)
> > at org.hsqldb.error.Error.error(Unknown Source)
> > at org.hsqldb.persist.Log.openLog(Unknown Source)
> > at org.hsqldb.persist.Log.open(Unknown Source)
> > at org.hsqldb.persist.Logger.open(Unknown Source)
> > at org.hsqldb.Database.reopen(Unknown Source)
> > at org.hsqldb.Database.open(Unknown Source)
> > at org.hsqldb.DatabaseManager.getDatabase(Unknown Source)
> > at org.hsqldb.DatabaseManager.newSession(Unknown Source)
> > ... 53 more
> >
> > Appreciate any inputs.
> >
> > Regards,
> >
> > Kalyani
> >
>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: Not able to run cTAKES UMLS in parallel [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Most likely. That is the old dictionary lookup, which keeps open access to a file database.
________________________________________
From: gandhi rajan <ga...@gmail.com>
Sent: Friday, January 11, 2019 12:39 PM
To: dev@ctakes.apache.org
Subject: Re: Not able to run cTAKES UMLS in parallel [EXTERNAL]
Hi, Have faced issues related to connectivity timeout using mysql db. But
never faced concurrency issue in our testing. Is it hsql db specific by any
chance?
On Friday, January 11, 2019, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Kalyani,
>
> At a guess, each parallel instance of ctakes is attempting to write some
> log file concurrently and the system does not approve.
>
> Have other people out there witnessed and overcome this problem?
>
> Sean
> ________________________________________
> From: Kalyani Unnikrishnan <ka...@hilabs.com>
> Sent: Friday, January 11, 2019 5:15 AM
> To: dev@ctakes.apache.org
> Subject: Not able to run cTAKES UMLS in parallel [EXTERNAL]
>
> Hi,
>
> I am trying to make cTAKES accessible by multiple programs in parallel. I
> was able to remove the error on umls.lck by setting PARAMS_ISOLATION to
> TRANSACTION_SERIALIZABLE. But I am still getting the following error when
> multiple programs are running the pipeline at the same time (it works fine
> if it is run in sequence).
>
> Caused by: java.sql.SQLException: file input/output error:
> org/apache/ctakes/dictionary/lookup/umls2011ab/umls.log
> at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
> at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
> at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source)
> at java.sql.DriverManager.getConnection(DriverManager.java:664)
> at java.sql.DriverManager.getConnection(DriverManager.java:247)
> at org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.
> load(JdbcConnectionResourceImpl.java:109)
> ... 47 more
> Caused by: org.hsqldb.HsqlException: file input/output error:
> org/apache/ctakes/dictionary/lookup/umls2011ab/umls.log
> at org.hsqldb.error.Error.error(Unknown Source)
> at org.hsqldb.error.Error.error(Unknown Source)
> at org.hsqldb.persist.Log.openLog(Unknown Source)
> at org.hsqldb.persist.Log.open(Unknown Source)
> at org.hsqldb.persist.Logger.open(Unknown Source)
> at org.hsqldb.Database.reopen(Unknown Source)
> at org.hsqldb.Database.open(Unknown Source)
> at org.hsqldb.DatabaseManager.getDatabase(Unknown Source)
> at org.hsqldb.DatabaseManager.newSession(Unknown Source)
> ... 53 more
>
> Appreciate any inputs.
>
> Regards,
>
> Kalyani
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: Not able to run cTAKES UMLS in parallel [EXTERNAL]
Posted by gandhi rajan <ga...@gmail.com>.
Hi, Have faced issues related to connectivity timeout using mysql db. But
never faced concurrency issue in our testing. Is it hsql db specific by any
chance?
On Friday, January 11, 2019, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Kalyani,
>
> At a guess, each parallel instance of ctakes is attempting to write some
> log file concurrently and the system does not approve.
>
> Have other people out there witnessed and overcome this problem?
>
> Sean
> ________________________________________
> From: Kalyani Unnikrishnan <ka...@hilabs.com>
> Sent: Friday, January 11, 2019 5:15 AM
> To: dev@ctakes.apache.org
> Subject: Not able to run cTAKES UMLS in parallel [EXTERNAL]
>
> Hi,
>
> I am trying to make cTAKES accessible by multiple programs in parallel. I
> was able to remove the error on umls.lck by setting PARAMS_ISOLATION to
> TRANSACTION_SERIALIZABLE. But I am still getting the following error when
> multiple programs are running the pipeline at the same time (it works fine
> if it is run in sequence).
>
> Caused by: java.sql.SQLException: file input/output error:
> org/apache/ctakes/dictionary/lookup/umls2011ab/umls.log
> at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
> at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
> at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source)
> at java.sql.DriverManager.getConnection(DriverManager.java:664)
> at java.sql.DriverManager.getConnection(DriverManager.java:247)
> at org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.
> load(JdbcConnectionResourceImpl.java:109)
> ... 47 more
> Caused by: org.hsqldb.HsqlException: file input/output error:
> org/apache/ctakes/dictionary/lookup/umls2011ab/umls.log
> at org.hsqldb.error.Error.error(Unknown Source)
> at org.hsqldb.error.Error.error(Unknown Source)
> at org.hsqldb.persist.Log.openLog(Unknown Source)
> at org.hsqldb.persist.Log.open(Unknown Source)
> at org.hsqldb.persist.Logger.open(Unknown Source)
> at org.hsqldb.Database.reopen(Unknown Source)
> at org.hsqldb.Database.open(Unknown Source)
> at org.hsqldb.DatabaseManager.getDatabase(Unknown Source)
> at org.hsqldb.DatabaseManager.newSession(Unknown Source)
> ... 53 more
>
> Appreciate any inputs.
>
> Regards,
>
> Kalyani
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"