[gridengine users] [SGE+sqlite3] Error: database is locked

Reuti reuti at staff.uni-marburg.de
Fri Nov 23 10:28:11 UTC 2012


Am 22.11.2012 um 21:27 schrieb Pierre LINDENBAUM:

>> Am 22.11.2012 um 17:24 schrieb Pierre Lindenbaum:
>> 
>>> I'm trying to run a script that fills a sqlite3 database.
>>> 
>>> The script creates a lock with `lockfile` , fills the database and
>>> releases the lock.
>>> 
>>> $cat test.sh
>>> 
>>> #!/bin/sh
>>> lockfile /commun/data/_tmp.idp448.lock
>>> sqlite3 /commun/data/stats.sqlite "create table if not exists
>>> timeBeginDB(target text UNIQUE NOT NULL,inserted int);"
>>> rm -f /commun/data/_tmp.idp448.lock
>>> whoami
>> 
>> Is "/commun/" shared between all nodes?
> 
> yes.
> 
> furthermore, *lockfile* is able to create the file
> /commun/data/_tmp.idp448.lock
> even when the script is called with 'qsub'
> 
> the lock file is later deleted with rm -f
> 
> only the call to sqlite3 prints an error message.
> 
>>> without qsub the script works without any problem :
>>> 
>>> [lindenb]$ sh test.sh
>>> lindenb
>>> 
>>> when qsub is invoked:
>>> 
>>> $ qsub -cwd -S /bin/sh test.sh
>>> Your job 673 ("test.sh") has been submitted
>>> 
>>> $ cat test.sh.o673
>>> lindenb
>>> 
>>> 
>>> $ cat test.sh.e673
>>> Error: database is locked
>>> 
>>> 
>>> which is a sqlite3 error.
>>> 
>>> Do you have any idea, suggestion of what, on the SGE side, could be the
>>> cause of that problem, this difference of behavior ?
>> 
>> Is the lockfile you define "_tmp.idp448.lock" in any way related to the
>> database?
> 
> no, it's a random name  I've created.  This file is here to ensure that
> only one process is accessing the sqlite3 database.
> 
> I'm the only one here playing with the cluster: so nobody can create the
> file on open the sqlite database at the very same time.
> 
>> Maybe the output is not telling the truth.
>> 
>> On the command line it runs local, but if it's submitted on any machine in
>> the cluster. Also the environment might miss some settings which are
>> present on the command line.
> 
> all the nodes have been installed using 'yum install sqlite3' so I guess
> there is nothing to configure.

Isn't it on the headnode working on a local file system (i.e. from the command line), but on a shared one from the node by the executing job?

-- Reuti



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