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From gandhi rajan <gandhiraja...@gmail.com>
Subject Re: Not able to run cTAKES UMLS in parallel [EXTERNAL]
Date Fri, 11 Jan 2019 17:39:53 GMT
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 <kalyani.unnikrishnan@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 !!!"

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