Completely agree. Kalyani, you could give it a try testing with MySQL DB. On Friday, January 11, 2019, Finan, Sean <[email protected]> wrote:
> Most likely. That is the old dictionary lookup, which keeps open access > to a file database. > ________________________________________ > From: gandhi rajan <[email protected]> > Sent: Friday, January 11, 2019 12:39 PM > To: [email protected] > 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 <[email protected] > > > 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 <[email protected]> > > Sent: Friday, January 11, 2019 5:15 AM > > To: [email protected] > > 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 !!!"
