opaltoolkit-users — Users mailing-list for Opal Toolkit

Re: [Opaltoolkit-users] Hibernate database connection

[Sriram K. <sr...@sd...>]

Hello Anthony,

I have committed your changes into SVN, and also added configuration  
and jars for c3p0 and mysql. I tested everything and it seems to be  
working fine. Please check out the latest version from SVN and let me  
know if there are any issues.

This will be part of the next Opal release that we are planning for  
end of this month. Thanks again for your contribution!

Cheers,
Sriram

On Sep 2, 2009, at 5:28 AM, Anthony Bretaudeau wrote:

> Hi!
> After testing, I've managed to make job exec time visualization work  
> with the following code (replace line 389 with it in src/edu/sdsc/ 
> nbcr/opal/dashboard/persistence/DBManager.java):
>
>         }else if  
> (dialect.equals("org.hibernate.dialect.MySQLDialect")){
>             //this is MySQL
>             query = "select jobInfo.start_time_date as date, " +
>                 //number of day
>                 " avg( ( last_update_date - start_time_date ) *  
> 86400 + " +
>                 //plus number of seconds (epoch returns seconds!)
>                 " ( time_to_sec(last_update_time) -  
> time_to_sec(start_time_time) )) as average " + queryTail;
>         }
>
> Feel free to include this in next release if it can help other users.
> Thanks.
> Anthony
>
> Anthony Bretaudeau a écrit :
>>
>> Oh yes, the exec time has a problem. I hadn't noticed that.
>> Is this the only SQL request using local SQL dialect? In this case,
>> something like "unix_timestamp( last_update_time -  
>> start_time_time ) as
>> average" should work for MySQL (copying the rest of the request from
>> PostgreSQL). If I have time, I'll try to test it.
>> Thanks
>> Anthony
>>
>> Luca Clementi a écrit :
>>
>>> Anthony Bretaudeau wrote:
>>>
>>>> Hi!
>>>> We've had a problem using MySQL database for storing opal2 jobs  
>>>> data
>>>> instead of the default HSQLDB.
>>>> It turned out it was a timeout problem which is quite well  
>>>> described
>>>> at the following address:
>>>> http://www.databasesandlife.com/automatic-reconnect-from-hibernate-to-mysql/ 
>>>> .
>>>> Briefly: mysql closes connection after an 8h timeout (which is  
>>>> quite
>>>> frequent for us, but not for servers where there is more activity).
>>>> We solved it by using c3p0 to manage database connection.
>>>> Here is what we have done to use it:
>>>>
>>>>
>>> Anthony,
>>> I expect the dashboard to have some problem visualizing the exec  
>>> time
>>> of your jobs.
>>>
>>> Have a look at line 365:
>>> http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/tags/opal2-core-2.0.0/src/edu/sdsc/nbcr/opal/dashboard/persistence/DBManager.java?revision=381&view=markup
>>>
>>>
>>> Unfortunately I could not find a way to make the query working using
>>> Hibernate SQL and I had to use the local SQL dialect.
>>>
>>> Given that I think we should start using some connection manager  
>>> since
>>> it is also recommended by the Hibernate guys.
>>>
>>> Sincerely,
>>> Luca
>>>
>>>
>>>> -Added c3p0 package in $opal_sources/lib/ and modified build.xml
>>>> consequently
>>>> -Created $opal_sources /etc/c3p0.properties and added "
>>>> c3p0.preferredTestQuery=SELECT 1; " in it.
>>>> -In build.xml, after <include name="OpalState.hbm.xml"/> added
>>>> <include name="c3p0.properties"/>
>>>> -In $OPAL_SOURCES/etc/hibernate-opal.cfg.xml, replaced:
>>>>
>>>>         <!-- JDBC connection pool (use the built-in) -->
>>>>         <!--<property name="connection.pool_size">1</property>-->
>>>>
>>>> By these lines:
>>>>
>>>>         <!-- JDBC connection pool (use c3p0) -->
>>>>         <property name="c3p0.min_size">1</property>
>>>>         <property name="c3p0.max_size">20</property>
>>>>         <property name="c3p0.timeout">1800</property>
>>>>         <property name="c3p0.max_statements">50</property>
>>>>         <property name="c3p0.idle_test_period">1800</property>
>>>>         <property
>>>> name 
>>>> = 
>>>> "connection 
>>>> .provider_class">org.hibernate.connection.C3P0ConnectionProvider</ 
>>>> property>
>>>>
>>>>
>>>> Maybe it would be a good idea to include it in a future version  
>>>> of opal?
>>>> Bye!
>>>>
>>>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports  
>> 2008 30-Day
>> trial. Simplify your report design, integration and deployment -  
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>> what you do best, core application coding. Discover what's new with
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>>
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> focus on
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Re: [Opaltoolkit-users] Hibernate database connection

[Anthony B. <ant...@ir...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi!<br>
After testing, I've managed to make job exec time visualization work
with the following code (replace line 389 with it in
src/edu/sdsc/nbcr/opal/dashboard/persistence/DBManager.java):<br>
<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; }else if (dialect.equals("org.hibernate.dialect.MySQLDialect")){<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; //this is MySQL<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; query = "select jobInfo.start_time_date as date, " +<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; //number of day <br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; " avg( ( last_update_date - start_time_date ) * 86400 +
" +<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; //plus number of seconds (epoch returns seconds!)<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; " ( time_to_sec(last_update_time) -
time_to_sec(start_time_time) )) as average " + queryTail;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; }<br>
<br>
Feel free to include this in next release if it can help other users.<br>
Thanks.<br>
Anthony<br>
<br>
Anthony Bretaudeau a &eacute;crit&nbsp;:
<blockquote cite="mid:4A9...@ir..." type="cite">
  <pre wrap="">Oh yes, the exec time has a problem. I hadn't noticed that.
Is this the only SQL request using local SQL dialect? In this case, 
something like "unix_timestamp( last_update_time - start_time_time ) as 
average" should work for MySQL (copying the rest of the request from 
PostgreSQL). If I have time, I'll try to test it.
Thanks
Anthony

Luca Clementi a &eacute;crit :
  </pre>
  <blockquote type="cite">
    <pre wrap="">Anthony Bretaudeau wrote:
    </pre>
    <blockquote type="cite">
      <pre wrap="">Hi!
We've had a problem using MySQL database for storing opal2 jobs data 
instead of the default HSQLDB.
It turned out it was a timeout problem which is quite well described 
at the following address: 
<a class="moz-txt-link-freetext" href="http://www.databasesandlife.com/automatic-reconnect-from-hibernate-to-mysql/">http://www.databasesandlife.com/automatic-reconnect-from-hibernate-to-mysql/</a>. 
Briefly: mysql closes connection after an 8h timeout (which is quite 
frequent for us, but not for servers where there is more activity).
We solved it by using c3p0 to manage database connection.
Here is what we have done to use it:

      </pre>
    </blockquote>
    <pre wrap="">
Anthony,
I expect the dashboard to have some problem visualizing the exec time 
of your jobs.

Have a look at line 365:
<a class="moz-txt-link-freetext" href="http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/tags/opal2-core-2.0.0/src/edu/sdsc/nbcr/opal/dashboard/persistence/DBManager.java?revision=381&view=markup">http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/tags/opal2-core-2.0.0/src/edu/sdsc/nbcr/opal/dashboard/persistence/DBManager.java?revision=381&amp;view=markup</a> 


Unfortunately I could not find a way to make the query working using 
Hibernate SQL and I had to use the local SQL dialect.

Given that I think we should start using some connection manager since 
it is also recommended by the Hibernate guys.

Sincerely,
Luca

    </pre>
    <blockquote type="cite">
      <pre wrap="">-Added c3p0 package in $opal_sources/lib/ and modified build.xml 
consequently
-Created $opal_sources /etc/c3p0.properties and added " 
c3p0.preferredTestQuery=SELECT 1; " in it.
-In build.xml, after &lt;include name="OpalState.hbm.xml"/&gt; added 
&lt;include name="c3p0.properties"/&gt;
-In $OPAL_SOURCES/etc/hibernate-opal.cfg.xml, replaced:

        &lt;!-- JDBC connection pool (use the built-in) --&gt;
        &lt;!--&lt;property name="connection.pool_size"&gt;1&lt;/property&gt;--&gt;

By these lines:

        &lt;!-- JDBC connection pool (use c3p0) --&gt;
        &lt;property name="c3p0.min_size"&gt;1&lt;/property&gt;
        &lt;property name="c3p0.max_size"&gt;20&lt;/property&gt;
        &lt;property name="c3p0.timeout"&gt;1800&lt;/property&gt;
        &lt;property name="c3p0.max_statements"&gt;50&lt;/property&gt;
        &lt;property name="c3p0.idle_test_period"&gt;1800&lt;/property&gt;
        &lt;property 
name="connection.provider_class"&gt;org.hibernate.connection.C3P0ConnectionProvider&lt;/property&gt; 


Maybe it would be a good idea to include it in a future version of opal?
Bye!

      </pre>
    </blockquote>
  </blockquote>
  <pre wrap=""><!---->
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</blockquote>
</body>
</html>

Re: [Opaltoolkit-users] Hibernate database connection

[Anthony B. <ant...@ir...>]

Oh yes, the exec time has a problem. I hadn't noticed that.
Is this the only SQL request using local SQL dialect? In this case, 
something like "unix_timestamp( last_update_time - start_time_time ) as 
average" should work for MySQL (copying the rest of the request from 
PostgreSQL). If I have time, I'll try to test it.
Thanks
Anthony

Luca Clementi a écrit :
> Anthony Bretaudeau wrote:
>> Hi!
>> We've had a problem using MySQL database for storing opal2 jobs data 
>> instead of the default HSQLDB.
>> It turned out it was a timeout problem which is quite well described 
>> at the following address: 
>> http://www.databasesandlife.com/automatic-reconnect-from-hibernate-to-mysql/. 
>> Briefly: mysql closes connection after an 8h timeout (which is quite 
>> frequent for us, but not for servers where there is more activity).
>> We solved it by using c3p0 to manage database connection.
>> Here is what we have done to use it:
>>
>
>
> Anthony,
> I expect the dashboard to have some problem visualizing the exec time 
> of your jobs.
>
> Have a look at line 365:
> http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/tags/opal2-core-2.0.0/src/edu/sdsc/nbcr/opal/dashboard/persistence/DBManager.java?revision=381&view=markup 
>
>
> Unfortunately I could not find a way to make the query working using 
> Hibernate SQL and I had to use the local SQL dialect.
>
> Given that I think we should start using some connection manager since 
> it is also recommended by the Hibernate guys.
>
> Sincerely,
> Luca
>
>> -Added c3p0 package in $opal_sources/lib/ and modified build.xml 
>> consequently
>> -Created $opal_sources /etc/c3p0.properties and added " 
>> c3p0.preferredTestQuery=SELECT 1; " in it.
>> -In build.xml, after <include name="OpalState.hbm.xml"/> added 
>> <include name="c3p0.properties"/>
>> -In $OPAL_SOURCES/etc/hibernate-opal.cfg.xml, replaced:
>>
>>         <!-- JDBC connection pool (use the built-in) -->
>>         <!--<property name="connection.pool_size">1</property>-->
>>
>> By these lines:
>>
>>         <!-- JDBC connection pool (use c3p0) -->
>>         <property name="c3p0.min_size">1</property>
>>         <property name="c3p0.max_size">20</property>
>>         <property name="c3p0.timeout">1800</property>
>>         <property name="c3p0.max_statements">50</property>
>>         <property name="c3p0.idle_test_period">1800</property>
>>         <property 
>> name="connection.provider_class">org.hibernate.connection.C3P0ConnectionProvider</property> 
>>
>>
>> Maybe it would be a good idea to include it in a future version of opal?
>> Bye!
>>
>

Re: [Opaltoolkit-users] opalUrl config

[Anthony B. <ant...@ir...>]

Ok, you're right, our server is not running on port 8080.
Maybe it would be a good idea to add it somewhere in the documentation?

Luca Clementi a écrit :
> Anthony Bretaudeau wrote:
>> Hi (again!)
>> When installing Opal a while back, I had to edit 
>> $opal_sources/webapps/opal2/WEB-INF/web.xml and change param-value of 
>> 'opalUrl' in order to have a working dashboard.
>> I was a bit confused as I didn't see this in the documentation and 
>> the comments in web.xml were not very encouraging ('Opal GUI config 
>> param... do not touch this').
>> I just wanted you to know about that. Is it a normal behaviour?
>> Thanks
>
> Anthony,
> if you shuts down the 8080 connector of your tomcat, then you have to 
> change the opalUrl with the new port you are using.
>
> That URL is used by Opal dashboard to query the AXIS admin interface 
> to get the list of services.
>
> Sincerely,
> Luca
>

Re: [Opaltoolkit-users] Hibernate database connection

[Luca C. <lcl...@uc...>]

Anthony Bretaudeau wrote:
> Hi!
> We've had a problem using MySQL database for storing opal2 jobs data 
> instead of the default HSQLDB.
> It turned out it was a timeout problem which is quite well described at 
> the following address: 
> http://www.databasesandlife.com/automatic-reconnect-from-hibernate-to-mysql/. 
> Briefly: mysql closes connection after an 8h timeout (which is quite 
> frequent for us, but not for servers where there is more activity).
> We solved it by using c3p0 to manage database connection.
> Here is what we have done to use it:
> 


Anthony,
I expect the dashboard to have some problem visualizing the exec time of 
your jobs.

Have a look at line 365:
http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/tags/opal2-core-2.0.0/src/edu/sdsc/nbcr/opal/dashboard/persistence/DBManager.java?revision=381&view=markup

Unfortunately I could not find a way to make the query working using 
Hibernate SQL and I had to use the local SQL dialect.

Given that I think we should start using some connection manager since 
it is also recommended by the Hibernate guys.

Sincerely,
Luca

> -Added c3p0 package in $opal_sources/lib/ and modified build.xml 
> consequently
> -Created $opal_sources /etc/c3p0.properties and added " 
> c3p0.preferredTestQuery=SELECT 1; " in it.
> -In build.xml, after <include name="OpalState.hbm.xml"/> added <include 
> name="c3p0.properties"/>
> -In $OPAL_SOURCES/etc/hibernate-opal.cfg.xml, replaced:
> 
>         <!-- JDBC connection pool (use the built-in) -->
>         <!--<property name="connection.pool_size">1</property>-->
> 
> By these lines:
> 
>         <!-- JDBC connection pool (use c3p0) -->
>         <property name="c3p0.min_size">1</property>
>         <property name="c3p0.max_size">20</property>
>         <property name="c3p0.timeout">1800</property>
>         <property name="c3p0.max_statements">50</property>
>         <property name="c3p0.idle_test_period">1800</property>
>         <property 
> name="connection.provider_class">org.hibernate.connection.C3P0ConnectionProvider</property>
> 
> Maybe it would be a good idea to include it in a future version of opal?
> Bye!
> 

Re: [Opaltoolkit-users] opalUrl config

[Luca C. <lcl...@uc...>]

Anthony Bretaudeau wrote:
> Hi (again!)
> When installing Opal a while back, I had to edit 
> $opal_sources/webapps/opal2/WEB-INF/web.xml and change param-value of 
> 'opalUrl' in order to have a working dashboard.
> I was a bit confused as I didn't see this in the documentation and the 
> comments in web.xml were not very encouraging ('Opal GUI config param... 
> do not touch this').
> I just wanted you to know about that. Is it a normal behaviour?
> Thanks

Anthony,
if you shuts down the 8080 connector of your tomcat, then you have to 
change the opalUrl with the new port you are using.

That URL is used by Opal dashboard to query the AXIS admin interface to 
get the list of services.

Sincerely,
Luca

Re: [Opaltoolkit-users] job data not being cleaned

[Malcolm T. <mt...@wu...>]

Wilfred,

Gotcha.

Thanks,
Malcolm

On Friday 28 August 2009 11:55:43 am Wilfred Li wrote:
> Hi, Malcolm,
>
> This part of job life time management is left to the administrators to set
> up a proper cron job to do the deletion. The value in opal.properties is
> only used to display on the dashboard and advise external users how long
> their data is maintained on the server. While Opal could manage this
> automatically, it's not implemented yet.
>
> Thanks
>
> Wilfred
>
>
> ________________________________________
> From: Malcolm Tobias [mt...@wu...]
> Sent: Friday, August 28, 2009 8:11 AM
> To: Opa...@li...
> Subject: [Opaltoolkit-users] job data not being cleaned
>
> I've got a working implementation of Opal 2.0 that I'm using for running
> PDB2PQR and APBS jobs.  Everything is running fine, but the job data isn't
> being cleared from the working directory.
>
> In my etc/opal.properties I have:
>
> # use this key to display how long to save user data on server
> opal.datalifetime=4 days
>
> and I don't see anywhere in the application-specific configuration files
> where this value is being over-ridden.
>
> I searched in the Tomcat directory and the only reference to this variable
> is also 4 days:
>
> /export/home/opal/jakarta-tomcat-5.0.30/webapps/opal2/WEB-INF/classes/opal.
>properties opal.datalifetime=4 days
>
> Yet none of the working directories appear to be getting deleted:
>
> [opal@sccne ROOT]$
> ls -l /export/home/opal/jakarta-tomcat-5.0.30/webapps/ROOT | less
> drwxrwxr-x  2 opal opal   4096 Aug 20 10:39 app1250782739797
> drwxrwxr-x  2 opal opal   4096 Aug 20 10:40 app1250782810226
> drwxrwxr-x  2 opal opal   4096 Aug 20 10:40 app1250782810359
> drwxrwxr-x  2 opal opal   4096 Aug 20 10:41 app1250782862526
> ...
>
> The catalina logs don't show any activity since the last time jobs have
> been run:
>
> [opal@sccne logs]$ tail  catalina.out
> 2009-08-24 12:37:34,074 INFO
> edu.sdsc.nbcr.opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUti
>l.java:213) - Updated status for job: app1250628292907
> 2009-08-24 12:37:34,078 ERROR
> edu.sdsc.nbcr.opal.AppServiceImpl$1.run(AppServiceImpl.java:657) -
> 2009-08-24 12:37:34,078 INFO
> edu.sdsc.nbcr.opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUti
>l.java:213) - Updated status for job: app1250628277496
> 2009-08-24 12:37:34,081 ERROR
> edu.sdsc.nbcr.opal.AppServiceImpl$1.run(AppServiceImpl.java:657) -
> 2009-08-24 12:37:34,086 INFO
> edu.sdsc.nbcr.opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUti
>l.java:213) - Updated status for job: app1250628288751
> 2009-08-24 12:37:34,090 ERROR
> edu.sdsc.nbcr.opal.AppServiceImpl$1.run(AppServiceImpl.java:657) -
>
> How are the job directories deleted?  Is the Tomcat server supposed to
> check periodically whether it's time to delete the directories?  How can I
> debug what's going wrong?
>
> Thanks,
> Malcolm
>
>
> --
> Malcolm Tobias
> 314.362.1594
>
>
> ---------------------------------------------------------------------------
>--- Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> 30-Day trial. Simplify your report design, integration and deployment - and
> focus on what you do best, core application coding. Discover what's new
> with Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users



-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] job data not being cleaned

[Wilfred Li <wi...@sd...>]

Hi, Malcolm,

This part of job life time management is left to the administrators to set up a proper cron job to do the deletion. The value in opal.properties is only used to display on the dashboard and advise external users how long their data is maintained on the server. While Opal could manage this automatically, it's not implemented yet.

Thanks

Wilfred


________________________________________
From: Malcolm Tobias [mt...@wu...]
Sent: Friday, August 28, 2009 8:11 AM
To: Opa...@li...
Subject: [Opaltoolkit-users] job data not being cleaned

I've got a working implementation of Opal 2.0 that I'm using for running
PDB2PQR and APBS jobs.  Everything is running fine, but the job data isn't
being cleared from the working directory.

In my etc/opal.properties I have:

# use this key to display how long to save user data on server
opal.datalifetime=4 days

and I don't see anywhere in the application-specific configuration files where
this value is being over-ridden.

I searched in the Tomcat directory and the only reference to this variable is
also 4 days:

/export/home/opal/jakarta-tomcat-5.0.30/webapps/opal2/WEB-INF/classes/opal.properties
opal.datalifetime=4 days

Yet none of the working directories appear to be getting deleted:

[opal@sccne ROOT]$
ls -l /export/home/opal/jakarta-tomcat-5.0.30/webapps/ROOT | less
drwxrwxr-x  2 opal opal   4096 Aug 20 10:39 app1250782739797
drwxrwxr-x  2 opal opal   4096 Aug 20 10:40 app1250782810226
drwxrwxr-x  2 opal opal   4096 Aug 20 10:40 app1250782810359
drwxrwxr-x  2 opal opal   4096 Aug 20 10:41 app1250782862526
...

The catalina logs don't show any activity since the last time jobs have been
run:

[opal@sccne logs]$ tail  catalina.out
2009-08-24 12:37:34,074 INFO
edu.sdsc.nbcr.opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java:213) -
Updated status for job: app1250628292907
2009-08-24 12:37:34,078 ERROR
edu.sdsc.nbcr.opal.AppServiceImpl$1.run(AppServiceImpl.java:657) -
2009-08-24 12:37:34,078 INFO
edu.sdsc.nbcr.opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java:213) -
Updated status for job: app1250628277496
2009-08-24 12:37:34,081 ERROR
edu.sdsc.nbcr.opal.AppServiceImpl$1.run(AppServiceImpl.java:657) -
2009-08-24 12:37:34,086 INFO
edu.sdsc.nbcr.opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java:213) -
Updated status for job: app1250628288751
2009-08-24 12:37:34,090 ERROR
edu.sdsc.nbcr.opal.AppServiceImpl$1.run(AppServiceImpl.java:657) -

How are the job directories deleted?  Is the Tomcat server supposed to check
periodically whether it's time to delete the directories?  How can I debug
what's going wrong?

Thanks,
Malcolm


--
Malcolm Tobias
314.362.1594


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[Opaltoolkit-users] job data not being cleaned

[Malcolm T. <mt...@wu...>]

I've got a working implementation of Opal 2.0 that I'm using for running 
PDB2PQR and APBS jobs.  Everything is running fine, but the job data isn't 
being cleared from the working directory.

In my etc/opal.properties I have:

# use this key to display how long to save user data on server
opal.datalifetime=4 days

and I don't see anywhere in the application-specific configuration files where 
this value is being over-ridden.

I searched in the Tomcat directory and the only reference to this variable is 
also 4 days:

/export/home/opal/jakarta-tomcat-5.0.30/webapps/opal2/WEB-INF/classes/opal.properties
opal.datalifetime=4 days

Yet none of the working directories appear to be getting deleted:

[opal@sccne ROOT]$ 
ls -l /export/home/opal/jakarta-tomcat-5.0.30/webapps/ROOT | less
drwxrwxr-x  2 opal opal   4096 Aug 20 10:39 app1250782739797
drwxrwxr-x  2 opal opal   4096 Aug 20 10:40 app1250782810226
drwxrwxr-x  2 opal opal   4096 Aug 20 10:40 app1250782810359
drwxrwxr-x  2 opal opal   4096 Aug 20 10:41 app1250782862526
...

The catalina logs don't show any activity since the last time jobs have been 
run:

[opal@sccne logs]$ tail  catalina.out 
2009-08-24 12:37:34,074 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java:213) - 
Updated status for job: app1250628292907
2009-08-24 12:37:34,078 ERROR 
edu.sdsc.nbcr.opal.AppServiceImpl$1.run(AppServiceImpl.java:657) - 
2009-08-24 12:37:34,078 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java:213) - 
Updated status for job: app1250628277496
2009-08-24 12:37:34,081 ERROR 
edu.sdsc.nbcr.opal.AppServiceImpl$1.run(AppServiceImpl.java:657) - 
2009-08-24 12:37:34,086 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java:213) - 
Updated status for job: app1250628288751
2009-08-24 12:37:34,090 ERROR 
edu.sdsc.nbcr.opal.AppServiceImpl$1.run(AppServiceImpl.java:657) - 

How are the job directories deleted?  Is the Tomcat server supposed to check 
periodically whether it's time to delete the directories?  How can I debug 
what's going wrong?

Thanks,
Malcolm


-- 
Malcolm Tobias
314.362.1594

[Opaltoolkit-users] opalUrl config

[Anthony B. <ant...@ir...>]

Hi (again!)
When installing Opal a while back, I had to edit 
$opal_sources/webapps/opal2/WEB-INF/web.xml and change param-value of 
'opalUrl' in order to have a working dashboard.
I was a bit confused as I didn't see this in the documentation and the 
comments in web.xml were not very encouraging ('Opal GUI config param... 
do not touch this').
I just wanted you to know about that. Is it a normal behaviour?
Thanks

[Opaltoolkit-users] Hibernate database connection

[Anthony B. <ant...@ir...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
</head>
<body bgcolor="#ffffff" text="#000000">
Hi!<br>
We've had a problem using MySQL database for storing opal2 jobs data
instead of the default HSQLDB.<br>
It turned out it was a timeout problem which is quite well described at
the following address:
<a class="moz-txt-link-freetext" href="http://www.databasesandlife.com/automatic-reconnect-from-hibernate-to-mysql/">http://www.databasesandlife.com/automatic-reconnect-from-hibernate-to-mysql/</a>.
Briefly: mysql closes connection after an 8h timeout (which is quite
frequent for us, but not for servers where there is more activity).<br>
We solved it by using c3p0 to manage database connection.<br>
Here is what we have done to use it:<br>
<br>
-Added c3p0 package in $opal_sources/lib/ and modified build.xml
consequently<br>
<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8">
<title></title>
<meta name="GENERATOR" content="OpenOffice.org 3.0  (Linux)">
<style type="text/css">
	<!--
		@page { margin: 2cm }
		P { margin-bottom: 0.21cm }
	--></style>
<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8">
<title></title>
<meta name="GENERATOR" content="OpenOffice.org 3.0  (Linux)">
<style type="text/css">
	<!--
		@page { margin: 2cm }
		P { margin-bottom: 0.21cm }
	--></style>-Created
$opal_sources /etc/c3p0.properties
and added " c3p0.preferredTestQuery=SELECT
1;
" in it.<br>
<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8">
<title></title>
<meta name="GENERATOR" content="OpenOffice.org 3.0  (Linux)">
<style type="text/css">!--
		@page { margin: 2cm }
		P { margin-bottom: 0.21cm }
	--&gt;</style>
<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8">
<title></title>
<meta name="GENERATOR" content="OpenOffice.org 3.0  (Linux)">
<style type="text/css">
	<!--
		@page { margin: 2cm }
		P { margin-bottom: 0.21cm }
	--></style>-In
build.xml, after &lt;include
name="OpalState.hbm.xml"/&gt; added &lt;include
name="c3p0.properties"/&gt;<br>
<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8">
<title></title>
<meta name="GENERATOR" content="OpenOffice.org 3.0  (Linux)">
<style type="text/css">
	<!--
		@page { margin: 2cm }
		P { margin-bottom: 0.21cm }
	-</style>-In
$OPAL_SOURCES/etc/hibernate-opal.cfg.xml, replaced:<br>
<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;!-- JDBC
connection pool (use the built-in) --&gt;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;!--&lt;property
name="connection.pool_size"&gt;1&lt;/property&gt;--&gt;
<br>
<br>
By these lines:<br>
<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8">
<title></title>
<meta name="GENERATOR" content="OpenOffice.org 3.0  (Linux)">
<style type="text/css">
	<!--
		@page { margin: 2cm }
		P { margin-bottom: 0.21cm }
	-cd</style><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;!-- JDBC connection pool (use c3p0) --&gt;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;property name="c3p0.min_size"&gt;1&lt;/property&gt;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;property name="c3p0.max_size"&gt;20&lt;/property&gt;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;property name="c3p0.timeout"&gt;1800&lt;/property&gt;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;property name="c3p0.max_statements"&gt;50&lt;/property&gt;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;property
name="c3p0.idle_test_period"&gt;1800&lt;/property&gt;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;property
name="connection.provider_class"&gt;org.hibernate.connection.C3P0ConnectionProvider&lt;/property&gt;<br>
<br>
Maybe it would be a good idea to include it in a future version of opal?<br>
Bye!<br>
<br>
</body>
</html>

Re: [Opaltoolkit-users] problem launching opal jobs

[Wilfred Li <wi...@sd...>]

That would be my suggestion as well. Is it possible for you to allow the opal user to submit to the default PBS queue first? 

Cheers,

Wilfred


-----Original Message-----
From: Luca Clementi [mailto:lcl...@uc...] 
Sent: Saturday, July 11, 2009 1:31 AM
To: Malcolm Tobias; opa...@li...
Subject: Re: [Opaltoolkit-users] problem launching opal jobs

Malcolm Tobias wrote:
> Olivier,
> 
> On Tuesday 30 June 2009 02:01:09 am osallou wrote:
>> are you sure your issue is not related to your job submission ?
> 
> I'm not.  In fact, I expect that this will likely fail until I figure out a 
> proper way to get a different default queue for the opal user under PBS.
> I was hoping to get everything else working first, then work out this final 
> point.  I was also hoping the error messages would help determine the current 
> problem.
> 

Tobias,
first you have to make sure that Opal user is able to submit job to PBS 
only after that you should try to debug this issue.

Sincerely,
Luca

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Re: [Opaltoolkit-users] problem launching opal jobs

[Luca C. <lcl...@uc...>]

Malcolm Tobias wrote:
> Olivier,
> 
> On Tuesday 30 June 2009 02:01:09 am osallou wrote:
>> are you sure your issue is not related to your job submission ?
> 
> I'm not.  In fact, I expect that this will likely fail until I figure out a 
> proper way to get a different default queue for the opal user under PBS.
> I was hoping to get everything else working first, then work out this final 
> point.  I was also hoping the error messages would help determine the current 
> problem.
> 

Tobias,
first you have to make sure that Opal user is able to submit job to PBS 
only after that you should try to debug this issue.

Sincerely,
Luca

Re: [Opaltoolkit-users] Problem reloading opal

[Luca C. <lcl...@uc...>]

Sriram Krishnan wrote:
> Hi Anthony,
> 
> I looks like you may have some old Opal classes from a previous
> version lying around - basically because it can't find the
> JobManagerType, which should be in the latest Opal jar.
> 
> There are two solutions to this problem. If you run "ant uninstall-
> all", it will go ahead and clean up all the old Opal jars from inside
> Tomcat. However, if you do this, all your deployed Opal services will
> be gone. You will have to install Opal again, and manually deploy them
> one by one.
> 
> The second option is you shut down tomcat, and run "ant upgrade". This
> should replace the old Opal jar with the new one, along with other
> prerequisite jars. I would try this option first, restart Tomcat and
> see if everything works. If it doesn't, you may have to try the brute
> force approach, which is option one.
> 
> Thanks, and let us know if that works.
> 
> Sriram

Hey,
my previous email wasn't very clear.... but I did some testing on 
stopping and restarting Opal webapp using tomcat manager interface.

For some reason it doesn't work (problem with log4j, and axis for some 
reason doesn't find mapping in the classpath), so at the moment it is 
not possible to stop and restart a Opal webapp.
At the moment you need to restart tomcat.

As soon as I get a chance I will take a look at this problem.


Sincerely,
Luca

Re: [Opaltoolkit-users] problem launching opal jobs

[Malcolm T. <mt...@wu...>]

Sriram,

On Monday 29 June 2009 12:57:08 pm Sriram Krishnan wrote:
> > Is there some way for me to increase the verbosity of the debugging?
>
> You can increase the Opal debugging by editing the lib/
> log4j.properties. You should change the line
> log4j.logger.edu.sdsc=WARN
> to
> log4j.logger.edu.sdsc=DEBUG
>
> After you do this, you will have to shut down tomcat, re-install Opal  
> (ant install) and restart Tomcat. You should get more debug messages  
> from Opal.
>
> Let us know if you see anything interesting with the increased logging  
> information.

It looks like it's already set to DEBUG:

[root@agave opal-ws-2.0]# grep log4j.logger.edu.sdsc lib/log4j.properties 
log4j.logger.edu.sdsc=DEBUG

Malcolm


-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] Problem reloading opal

[Sriram K. <sr...@sd...>]

Hi Anthony,

I looks like you may have some old Opal classes from a previous  
version lying around - basically because it can't find the  
JobManagerType, which should be in the latest Opal jar.

There are two solutions to this problem. If you run "ant uninstall- 
all", it will go ahead and clean up all the old Opal jars from inside  
Tomcat. However, if you do this, all your deployed Opal services will  
be gone. You will have to install Opal again, and manually deploy them  
one by one.

The second option is you shut down tomcat, and run "ant upgrade". This  
should replace the old Opal jar with the new one, along with other  
prerequisite jars. I would try this option first, restart Tomcat and  
see if everything works. If it doesn't, you may have to try the brute  
force approach, which is option one.

Thanks, and let us know if that works.

Sriram

On Jul 7, 2009, at 2:34 AM, Anthony Bretaudeau wrote:

> Hi!
> Here's a more detailed log (debug level). Hope it will help you.
> Tell me if you need more info.
> Thanks
> Anthony
>
> Luca Clementi a écrit :
>> Anthony Bretaudeau wrote:
>>> Hi,
>>> We're using edu.sdsc.nbcr.opal.manager.DRMAAJobManager (slightly  
>>> modified to work with DRMAA.jar 6.1, but the changes are minor).
>>> Issuing ant clean and ant install didn't solved the problem.
>>> Here's a full log of a tomcat session with the following actions:  
>>> started tomcat, launched a job (which worked), stopped opal2,  
>>> wait, restarted opal2, launched a job
>>>
>>
>> Dear Anthony,
>>
>>> Exception in thread "HSQLDB Timer @609a18a0"  
>>> java.lang.NullPointerException      <----- this is when I "Stop"  
>>> opal2
>>>    at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
>>>    at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
>>>    at java.lang.Thread.run(Thread.java:595)
>>
>> We know this error, and we have seen this in every installation we  
>> have here, every time we shutdown tomcat.
>>
>> Since this is a very generic error and it doesn't have any impact  
>> on our DBs, we haven't fixed it.
>>
>>> "Start" opal2 after a moment (no log) and I launch a job (no log  
>>> here but a SOAP fault received by clients)
>>
>> This is very weird, if opal2 starts properly it must print some  
>> log, on my installation I could get some ClassNotFound errors when  
>> trying to restart a stopped application from the manager interface.
>>
>> Right now Im out of town when I will be back I'll take a look at  
>> this problem.
>>
>>
>> Sincerely,
>> Luca
>>
>>
>>
>>
>>
>>
>>
>> 2009-07-03 06:57:34,043 ERROR  
>> org 
>> .apache 
>> .axis 
>> .configuration 
>> .EngineConfigurationFactoryServlet 
>> .getServerEngineConfig(EngineConfigurationFactoryServlet.java:162)  
>> - Unable to find config file.  Creating new servlet engine config  
>> file: /WEB-INF/server-config.wsdd
>> 2009-07-03 06:57:34,093 ERROR  
>> org 
>> .apache 
>> .axis 
>> .deployment.wsdd.WSDDService.deployTypeMapping(WSDDService.java: 
>> 560) - Unable to deploy typemapping: {http://nbcr.sdsc.edu/opal/ 
>> types}JobManagerType
>> java.lang.ClassNotFoundException: edu.sdsc.nbcr.opal.JobManagerType
>>    at  
>> org 
>> .apache 
>> .catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java: 
>> 1359)
>>    at  
>> org 
>> .apache 
>> .catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java: 
>> 1205)
>>    at org.apache.axis.utils.ClassUtils$2.run(ClassUtils.java:186)
>>    at java.security.AccessController.doPrivileged(Native Method)
>>    at org.apache.axis.utils.ClassUtils.loadClass(ClassUtils.java:160)
>>    at org.apache.axis.utils.ClassUtils.forName(ClassUtils.java:100)
>>    at  
>> org 
>> .apache 
>> .axis 
>> .deployment 
>> .wsdd.WSDDTypeMapping.getLanguageSpecificType(WSDDTypeMapping.java: 
>> 183)
>>    at  
>> org 
>> .apache 
>> .axis 
>> .deployment.wsdd.WSDDService.deployTypeMapping(WSDDService.java:542)
>>    at  
>> org 
>> .apache.axis.deployment.wsdd.WSDDService.initTMR(WSDDService.java: 
>> 253)
>>    at  
>> org.apache.axis.deployment.wsdd.WSDDService.<init>(WSDDService.java: 
>> 233)
>>    at  
>> org 
>> .apache 
>> .axis.deployment.wsdd.WSDDDeployment.<init>(WSDDDeployment.java:192)
>>    at  
>> org 
>> .apache 
>> .axis.deployment.wsdd.WSDDDocument.setDocument(WSDDDocument.java:139)
>>    at  
>> org 
>> .apache.axis.deployment.wsdd.WSDDDocument.<init>(WSDDDocument.java: 
>> 65)
>>    at  
>> org 
>> .apache 
>> .axis.configuration.FileProvider.configureEngine(FileProvider.java: 
>> 179)
>>    at org.apache.axis.AxisEngine.init(AxisEngine.java:172)
>>    at org.apache.axis.AxisEngine.<init>(AxisEngine.java:156)
>>    at org.apache.axis.server.AxisServer.<init>(AxisServer.java:88)
>>    at  
>> org 
>> .apache 
>> .axis 
>> .server 
>> .DefaultAxisServerFactory 
>> .createServer(DefaultAxisServerFactory.java:109)
>>    at  
>> org 
>> .apache 
>> .axis 
>> .server 
>> .DefaultAxisServerFactory.getServer(DefaultAxisServerFactory.java:73)
>>    at org.apache.axis.server.AxisServer.getServer(AxisServer.java:73)
>>    at  
>> org 
>> .apache 
>> .axis.transport.http.AxisServletBase.getEngine(AxisServletBase.java: 
>> 185)
>>    at  
>> org 
>> .apache 
>> .axis.transport.http.AxisServletBase.getOption(AxisServletBase.java: 
>> 396)
>>    at  
>> org 
>> .apache 
>> .axis.transport.http.AxisServletBase.init(AxisServletBase.java:112)
>>    at  
>> org.apache.axis.transport.http.AxisServlet.init(AxisServlet.java:156)
>>    at javax.servlet.GenericServlet.init(GenericServlet.java:212)
>>    at  
>> org 
>> .apache 
>> .catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139)
>>    at  
>> org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java: 
>> 966)
>>    at  
>> org 
>> .apache 
>> .catalina.core.StandardContext.loadOnStartup(StandardContext.java: 
>> 3956)
>>    at  
>> org.apache.catalina.core.StandardContext.start(StandardContext.java: 
>> 4230)
>>    at  
>> org 
>> .apache.catalina.manager.ManagerServlet.start(ManagerServlet.java: 
>> 1176)
>>    at  
>> org 
>> .apache 
>> .catalina.manager.HTMLManagerServlet.start(HTMLManagerServlet.java: 
>> 542)
>>    at  
>> org 
>> .apache 
>> .catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java: 
>> 105)
>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>>    at  
>> org 
>> .apache 
>> .catalina 
>> .core 
>> .ApplicationFilterChain 
>> .internalDoFilter(ApplicationFilterChain.java:269)
>>    at  
>> org 
>> .apache 
>> .catalina 
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>> 188)
>>    at  
>> org 
>> .apache 
>> .catalina 
>> .core.StandardWrapperValve.invoke(StandardWrapperValve.java:210)
>>    at  
>> org 
>> .apache 
>> .catalina 
>> .core.StandardContextValve.invoke(StandardContextValve.java:174)
>>    at  
>> org 
>> .apache 
>> .catalina 
>> .authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525)
>>    at  
>> org 
>> .apache 
>> .catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
>>    at  
>> org 
>> .apache 
>> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
>>    at  
>> org 
>> .apache 
>> .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java: 
>> 108)
>>    at  
>> org 
>> .apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java: 
>> 151)
>>    at  
>> org 
>> .apache.coyote.http11.Http11Processor.process(Http11Processor.java: 
>> 870)
>>    at org.apache.coyote.http11.Http11BaseProtocol 
>> $Http11ConnectionHandler.processConnection(Http11BaseProtocol.java: 
>> 665)
>>    at  
>> org 
>> .apache 
>> .tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java: 
>> 528)
>>    at  
>> org 
>> .apache 
>> .tomcat 
>> .util 
>> .net 
>> .LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
>>    at org.apache.tomcat.util.threads.ThreadPool 
>> $ControlRunnable.run(ThreadPool.java:685)
>>
> [First try: successful job launching]
> 2009.07.07 08:59:42,355 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.launchJobBlocking(AppServiceImpl.java: 
> 270) - called
> 2009.07.07 08:59:42,356 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1038) - called
> 2009.07.07 08:59:42,382 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java: 
> 944) - called
> 2009.07.07 08:59:42,405 INFO   
> edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's  
> DN: Unknown client
> 2009.07.07 08:59:42,405 INFO   
> edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's  
> IP: 127.0.0.1
> 2009.07.07 08:59:42,405 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java: 
> 72) - called
> 2009.07.07 08:59:42,424 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579)  
> - Using job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
> 2009.07.07 08:59:42,424 INFO   
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.initialize(DRMAAJobManager.java: 
> 64) - called
> 2009.07.07 08:59:42,424 INFO   
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 103) - called
> 2009.07.07 08:59:42,425 DEBUG  
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 125) - Argument list: [arg list not very interesting in this log]
> 2009.07.07 08:59:42,425 DEBUG  
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 182) - CMD: [cmd line not very interesting in this log]
> 2009.07.07 08:59:42,425 INFO   
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 207) - All jobs have a hard limit of 3600 seconds
> 2009.07.07 08:59:42,426 DEBUG  
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 212) - Working directory: /[...]/opal/app1246957182356/
> 2009.07.07 08:59:42,426 ERROR  
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 230) - Can't set hard limit - The hardRunDurationLimit attribute is  
> not supported.
> 2009.07.07 08:59:42,434 INFO   
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 235) - DRMAA job has been submitted with id 1183942
> 2009.07.07 08:59:42,434 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.manager.DRMAAJobManager.waitForActivation(DRMAAJobManager.java: 
> 259) - called
> 2009.07.07 08:59:57,460 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 161) - called
> 2009.07.07 08:59:57,460 DEBUG  
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 162) - Updating status to: Execution in progress
> 2009.07.07 08:59:57,477 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 213) - Updated status for job: app1246957182356
> 2009.07.07 08:59:57,477 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.manager.DRMAAJobManager.waitForCompletion(DRMAAJobManager.java: 
> 304) - called
> 2009.07.07 09:00:06,655 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 136) - called
> 2009.07.07 09:00:06,655 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 161) - called
> 2009.07.07 09:00:06,656 DEBUG  
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 162) - Updating status to: Writing output metadata
> 2009.07.07 09:00:06,668 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 213) - Updated status for job: app1246957182356
> 2009.07.07 09:00:06,672 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.saveOutputsInDatabase(HibernateUtil.java: 
> 234) - called
> 2009.07.07 09:00:06,676 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 161) - called
> 2009.07.07 09:00:06,676 DEBUG  
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 162) - Updating status to: Execution complete - check outputs to  
> verify successful execution
> 2009.07.07 09:00:06,691 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 213) - Updated status for job: app1246957182356
> 2009.07.07 09:00:06,692 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.manageJob(AppServiceImpl.java:938)  
> - Execution complete for job: app1246957182356
> 2009.07.07 09:00:06,692 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.queryStatus(AppServiceImpl.java: 
> 300) - called for job: app1246957182356
> 2009.07.07 09:00:06,692 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1038) - called
> 2009.07.07 09:00:06,693 INFO   
> edu.sdsc.nbcr.opal.state.HibernateUtil.getStatus(HibernateUtil.java: 
> 291) - called
> 2009.07.07 09:00:06,694 DEBUG  
> edu.sdsc.nbcr.opal.AppServiceImpl.queryStatus(AppServiceImpl.java: 
> 316) - Query execution time: 2 ms
> 2009.07.07 09:00:06,694 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.getOutputs(AppServiceImpl.java: 
> 361) - called for job: app1246957182356
> 2009.07.07 09:00:06,695 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1038) - called
> 2009.07.07 09:00:06,695 INFO   
> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java: 
> 404) - called
> 2009.07.07 09:00:06,706 DEBUG  
> edu.sdsc.nbcr.opal.AppServiceImpl.getOutputs(AppServiceImpl.java: 
> 384) - Output retrieval time: 12 ms
> 2009.07.07 09:00:06,706 DEBUG  
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.launchJobBlocking(AppServiceImpl.java: 
> 286) - Server execution time: 24351 ms
>
>
> [stop then restart opal2 webapp]
> 2009.07.07 09:01:29,518 INFO   
> edu 
> .sdsc 
> .nbcr.opal.dashboard.servlet.OpalServices.init(OpalServices.java:68)  
> - Loading OpalServices (init method).
> 2009.07.07 09:01:29,523 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java: 
> 61) - Loading OpalInfoServlet (init method).
>
>
> [first job launching: fails]
> 2009.07.07 09:02:02,900 DEBUG  
> edu.sdsc.nbcr.opal.AppServiceImpl.<clinit>(AppServiceImpl.java:133)  
> - Checking if there are any zombie jobs
> 2009.07.07 09:02:02,901 INFO   
> edu 
> .sdsc 
> .nbcr.opal.state.HibernateUtil.markZombieJobs(HibernateUtil.java:94)  
> - called
> 2009.07.07 09:02:03,089 DEBUG  
> edu.sdsc.nbcr.opal.AppServiceImpl.<clinit>(AppServiceImpl.java:137)  
> - Number of DB entries for zombie jobs cleaned up: 0
> 2009.07.07 09:02:03,133 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.<init>(AppServiceImpl.java:172) -  
> called
> 2009.07.07 09:02:03,162 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.launchJobBlocking(AppServiceImpl.java: 
> 270) - called
> 2009.07.07 09:02:03,162 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1038) - called
> 2009.07.07 09:02:03,163 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1068) - Configuring service for the first time
> 2009.07.07 09:02:03,163 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1072) - Reading application config: /[...]/opal-ws-2.0/configs/ 
> bioquali_config.xml
> 2009.07.07 09:02:03,164 DEBUG  
> edu.sdsc.nbcr.common.TypeDeserializer.getValue(TypeDeserializer.java: 
> 50) - called
> 2009.07.07 09:02:03,220 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java: 
> 944) - called
> 2009.07.07 09:02:03,229 INFO   
> edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's  
> DN: Unknown client
> 2009.07.07 09:02:03,229 INFO   
> edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's  
> IP: 127.0.0.1
> 2009.07.07 09:02:03,230 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java: 
> 72) - called
> 2009.07.07 09:02:03,247 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579)  
> - Using job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
>
>
> [second job launching: fails]
> 2009.07.07 09:03:10,656 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.launchJobBlocking(AppServiceImpl.java: 
> 270) - called
> 2009.07.07 09:03:10,656 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1038) - called
> 2009.07.07 09:03:10,660 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java: 
> 944) - called
> 2009.07.07 09:03:10,667 INFO   
> edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's  
> DN: Unknown client
> 2009.07.07 09:03:10,667 INFO   
> edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's  
> IP: 127.0.0.1
> 2009.07.07 09:03:10,668 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java: 
> 72) - called
> 2009.07.07 09:03:10,669 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579)  
> - Using job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
>
> [tomcat restart]
> 2009.07.07 09:08:33,652 INFO   
> edu 
> .sdsc 
> .nbcr.opal.dashboard.servlet.OpalServices.init(OpalServices.java:68)  
> - Loading OpalServices (init method).
> 2009.07.07 09:08:33,657 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java: 
> 61) - Loading OpalInfoServlet (init method).
>
> [successful job launching after tomcat restart]
> 2009.07.07 09:11:51,266 DEBUG  
> edu.sdsc.nbcr.opal.AppServiceImpl.<clinit>(AppServiceImpl.java:133)  
> - Checking if there are any zombie jobs
> 2009.07.07 09:11:51,267 INFO   
> edu 
> .sdsc 
> .nbcr.opal.state.HibernateUtil.markZombieJobs(HibernateUtil.java:94)  
> - called
> 2009.07.07 09:11:51,394 DEBUG  
> edu.sdsc.nbcr.opal.AppServiceImpl.<clinit>(AppServiceImpl.java:137)  
> - Number of DB entries for zombie jobs cleaned up: 2
> 2009.07.07 09:11:51,443 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.<init>(AppServiceImpl.java:172) -  
> called
> 2009.07.07 09:11:51,476 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.launchJobBlocking(AppServiceImpl.java: 
> 270) - called
> 2009.07.07 09:11:51,476 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1038) - called
> 2009.07.07 09:11:51,477 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1068) - Configuring service for the first time
> 2009.07.07 09:11:51,477 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1072) - Reading application config: /[...]/opal-ws-2.0/configs/ 
> bioquali_config.xml
> 2009.07.07 09:11:51,478 DEBUG  
> edu.sdsc.nbcr.common.TypeDeserializer.getValue(TypeDeserializer.java: 
> 50) - called
> 2009.07.07 09:11:51,590 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java: 
> 944) - called
> 2009.07.07 09:11:51,600 INFO   
> edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's  
> DN: Unknown client
> 2009.07.07 09:11:51,600 INFO   
> edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's  
> IP: 127.0.0.1
> 2009.07.07 09:11:51,600 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java: 
> 72) - called
> 2009.07.07 09:11:51,620 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579)  
> - Using job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
> 2009.07.07 09:11:51,846 INFO   
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.initialize(DRMAAJobManager.java: 
> 64) - called
> 2009.07.07 09:11:51,847 INFO   
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 103) - called
> 2009.07.07 09:11:51,847 DEBUG  
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 125) - Argument list: [arg list not very interesting in this log]
> 2009.07.07 09:11:51,847 DEBUG  
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 182) - CMD: [cmd line not very interesting in this log]
> 2009.07.07 09:11:51,848 INFO   
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 207) - All jobs have a hard limit of 3600 seconds
> 2009.07.07 09:11:51,849 DEBUG  
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 212) - Working directory: /[...]/www-tmp/opal/app1246957911532/
> 2009.07.07 09:11:51,853 ERROR  
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 230) - Can't set hard limit - The hardRunDurationLimit attribute is  
> not supported.
> 2009.07.07 09:11:51,858 INFO   
> edu 
> .sdsc 
> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: 
> 235) - DRMAA job has been submitted with id 1183943
> 2009.07.07 09:11:51,858 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.manager.DRMAAJobManager.waitForActivation(DRMAAJobManager.java: 
> 259) - called
> 2009.07.07 09:11:57,870 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 161) - called
> 2009.07.07 09:11:57,870 DEBUG  
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 162) - Updating status to: Execution in progress
> 2009.07.07 09:11:57,890 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 213) - Updated status for job: app1246957911532
> 2009.07.07 09:11:57,890 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.manager.DRMAAJobManager.waitForCompletion(DRMAAJobManager.java: 
> 304) - called
> 2009.07.07 09:12:02,763 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 136) - called
> 2009.07.07 09:12:02,763 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 161) - called
> 2009.07.07 09:12:02,764 DEBUG  
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 162) - Updating status to: Writing output metadata
> 2009.07.07 09:12:02,778 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 213) - Updated status for job: app1246957911532
> 2009.07.07 09:12:02,781 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.saveOutputsInDatabase(HibernateUtil.java: 
> 234) - called
> 2009.07.07 09:12:02,801 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 161) - called
> 2009.07.07 09:12:02,801 DEBUG  
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 162) - Updating status to: Execution complete - check outputs to  
> verify successful execution
> 2009.07.07 09:12:02,819 INFO   
> edu 
> .sdsc 
> .nbcr 
> .opal.state.HibernateUtil.updateJobInfoInDatabase(HibernateUtil.java: 
> 213) - Updated status for job: app1246957911532
> 2009.07.07 09:12:02,820 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.manageJob(AppServiceImpl.java:938)  
> - Execution complete for job: app1246957911532
> 2009.07.07 09:12:02,820 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.queryStatus(AppServiceImpl.java: 
> 300) - called for job: app1246957911532
> 2009.07.07 09:12:02,821 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1038) - called
> 2009.07.07 09:12:02,821 INFO   
> edu.sdsc.nbcr.opal.state.HibernateUtil.getStatus(HibernateUtil.java: 
> 291) - called
> 2009.07.07 09:12:02,823 DEBUG  
> edu.sdsc.nbcr.opal.AppServiceImpl.queryStatus(AppServiceImpl.java: 
> 316) - Query execution time: 3 ms
> 2009.07.07 09:12:02,823 INFO   
> edu.sdsc.nbcr.opal.AppServiceImpl.getOutputs(AppServiceImpl.java: 
> 361) - called for job: app1246957911532
> 2009.07.07 09:12:02,823 INFO   
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java: 
> 1038) - called
> 2009.07.07 09:12:02,824 INFO   
> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java: 
> 404) - called
> 2009.07.07 09:12:02,849 DEBUG  
> edu.sdsc.nbcr.opal.AppServiceImpl.getOutputs(AppServiceImpl.java: 
> 384) - Output retrieval time: 26 ms
> 2009.07.07 09:12:02,850 DEBUG  
> edu 
> .sdsc.nbcr.opal.AppServiceImpl.launchJobBlocking(AppServiceImpl.java: 
> 286) - Server execution time: 11374 ms
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
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Re: [Opaltoolkit-users] Problem reloading opal

[Anthony B. <ant...@ir...>]

Hi!
Here's a more detailed log (debug level). Hope it will help you.
Tell me if you need more info.
Thanks
Anthony

Luca Clementi a écrit :
> Anthony Bretaudeau wrote:
>> Hi,
>> We're using edu.sdsc.nbcr.opal.manager.DRMAAJobManager (slightly 
>> modified to work with DRMAA.jar 6.1, but the changes are minor).
>> Issuing ant clean and ant install didn't solved the problem.
>> Here's a full log of a tomcat session with the following actions: 
>> started tomcat, launched a job (which worked), stopped opal2, wait, 
>> restarted opal2, launched a job
>>
>
> Dear Anthony,
>
>> Exception in thread "HSQLDB Timer @609a18a0" 
>> java.lang.NullPointerException      <----- this is when I "Stop" opal2
>>     at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
>>     at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
>>     at java.lang.Thread.run(Thread.java:595)
>
> We know this error, and we have seen this in every installation we 
> have here, every time we shutdown tomcat.
>
> Since this is a very generic error and it doesn't have any impact on 
> our DBs, we haven't fixed it.
>
>> "Start" opal2 after a moment (no log) and I launch a job (no log here 
>> but a SOAP fault received by clients)
>
> This is very weird, if opal2 starts properly it must print some log, 
> on my installation I could get some ClassNotFound errors when trying 
> to restart a stopped application from the manager interface.
>
> Right now Im out of town when I will be back I'll take a look at this 
> problem.
>
>
> Sincerely,
> Luca
>
>
>
>
>
>
>
> 2009-07-03 06:57:34,043 ERROR 
> org.apache.axis.configuration.EngineConfigurationFactoryServlet.getServerEngineConfig(EngineConfigurationFactoryServlet.java:162) 
> - Unable to find config file.  Creating new servlet engine config 
> file: /WEB-INF/server-config.wsdd
> 2009-07-03 06:57:34,093 ERROR 
> org.apache.axis.deployment.wsdd.WSDDService.deployTypeMapping(WSDDService.java:560) 
> - Unable to deploy typemapping: 
> {http://nbcr.sdsc.edu/opal/types}JobManagerType
> java.lang.ClassNotFoundException: edu.sdsc.nbcr.opal.JobManagerType
>     at 
> org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1359) 
>
>     at 
> org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1205) 
>
>     at org.apache.axis.utils.ClassUtils$2.run(ClassUtils.java:186)
>     at java.security.AccessController.doPrivileged(Native Method)
>     at org.apache.axis.utils.ClassUtils.loadClass(ClassUtils.java:160)
>     at org.apache.axis.utils.ClassUtils.forName(ClassUtils.java:100)
>     at 
> org.apache.axis.deployment.wsdd.WSDDTypeMapping.getLanguageSpecificType(WSDDTypeMapping.java:183) 
>
>     at 
> org.apache.axis.deployment.wsdd.WSDDService.deployTypeMapping(WSDDService.java:542) 
>
>     at 
> org.apache.axis.deployment.wsdd.WSDDService.initTMR(WSDDService.java:253)
>     at 
> org.apache.axis.deployment.wsdd.WSDDService.<init>(WSDDService.java:233)
>     at 
> org.apache.axis.deployment.wsdd.WSDDDeployment.<init>(WSDDDeployment.java:192) 
>
>     at 
> org.apache.axis.deployment.wsdd.WSDDDocument.setDocument(WSDDDocument.java:139) 
>
>     at 
> org.apache.axis.deployment.wsdd.WSDDDocument.<init>(WSDDDocument.java:65)
>     at 
> org.apache.axis.configuration.FileProvider.configureEngine(FileProvider.java:179) 
>
>     at org.apache.axis.AxisEngine.init(AxisEngine.java:172)
>     at org.apache.axis.AxisEngine.<init>(AxisEngine.java:156)
>     at org.apache.axis.server.AxisServer.<init>(AxisServer.java:88)
>     at 
> org.apache.axis.server.DefaultAxisServerFactory.createServer(DefaultAxisServerFactory.java:109) 
>
>     at 
> org.apache.axis.server.DefaultAxisServerFactory.getServer(DefaultAxisServerFactory.java:73) 
>
>     at org.apache.axis.server.AxisServer.getServer(AxisServer.java:73)
>     at 
> org.apache.axis.transport.http.AxisServletBase.getEngine(AxisServletBase.java:185) 
>
>     at 
> org.apache.axis.transport.http.AxisServletBase.getOption(AxisServletBase.java:396) 
>
>     at 
> org.apache.axis.transport.http.AxisServletBase.init(AxisServletBase.java:112) 
>
>     at 
> org.apache.axis.transport.http.AxisServlet.init(AxisServlet.java:156)
>     at javax.servlet.GenericServlet.init(GenericServlet.java:212)
>     at 
> org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) 
>
>     at 
> org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
>     at 
> org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) 
>
>     at 
> org.apache.catalina.core.StandardContext.start(StandardContext.java:4230)
>     at 
> org.apache.catalina.manager.ManagerServlet.start(ManagerServlet.java:1176) 
>
>     at 
> org.apache.catalina.manager.HTMLManagerServlet.start(HTMLManagerServlet.java:542) 
>
>     at 
> org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:105) 
>
>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>     at 
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) 
>
>     at 
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) 
>
>     at 
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210) 
>
>     at 
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) 
>
>     at 
> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525) 
>
>     at 
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) 
>
>     at 
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) 
>
>     at 
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) 
>
>     at 
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151) 
>
>     at 
> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870) 
>
>     at 
> org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) 
>
>     at 
> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) 
>
>     at 
> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) 
>
>     at 
> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685) 
>
>

Re: [Opaltoolkit-users] Problem reloading opal

[Luca C. <lcl...@uc...>]

Anthony Bretaudeau wrote:
> Hi,
> We're using edu.sdsc.nbcr.opal.manager.DRMAAJobManager (slightly 
> modified to work with DRMAA.jar 6.1, but the changes are minor).
> Issuing ant clean and ant install didn't solved the problem.
> Here's a full log of a tomcat session with the following actions: 
> started tomcat, launched a job (which worked), stopped opal2, wait, 
> restarted opal2, launched a job
> 

Dear Anthony,

> Exception in thread "HSQLDB Timer @609a18a0" 
> java.lang.NullPointerException      <----- this is when I "Stop" opal2
>     at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
>     at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
>     at java.lang.Thread.run(Thread.java:595)

We know this error, and we have seen this in every installation we have 
here, every time we shutdown tomcat.

Since this is a very generic error and it doesn't have any impact on our 
DBs, we haven't fixed it.

> "Start" opal2 after a moment (no log) and I launch a job (no log here 
> but a SOAP fault received by clients)

This is very weird, if opal2 starts properly it must print some log, on 
my installation I could get some ClassNotFound errors when trying to 
restart a stopped application from the manager interface.

Right now Im out of town when I will be back I'll take a look at this 
problem.


Sincerely,
Luca







2009-07-03 06:57:34,043 ERROR 
org.apache.axis.configuration.EngineConfigurationFactoryServlet.getServerEngineConfig(EngineConfigurationFactoryServlet.java:162) 
- Unable to find config file.  Creating new servlet engine config file: 
/WEB-INF/server-config.wsdd
2009-07-03 06:57:34,093 ERROR 
org.apache.axis.deployment.wsdd.WSDDService.deployTypeMapping(WSDDService.java:560) 
- Unable to deploy typemapping: 
{http://nbcr.sdsc.edu/opal/types}JobManagerType
java.lang.ClassNotFoundException: edu.sdsc.nbcr.opal.JobManagerType
	at 
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1359)
	at 
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1205)
	at org.apache.axis.utils.ClassUtils$2.run(ClassUtils.java:186)
	at java.security.AccessController.doPrivileged(Native Method)
	at org.apache.axis.utils.ClassUtils.loadClass(ClassUtils.java:160)
	at org.apache.axis.utils.ClassUtils.forName(ClassUtils.java:100)
	at 
org.apache.axis.deployment.wsdd.WSDDTypeMapping.getLanguageSpecificType(WSDDTypeMapping.java:183)
	at 
org.apache.axis.deployment.wsdd.WSDDService.deployTypeMapping(WSDDService.java:542)
	at 
org.apache.axis.deployment.wsdd.WSDDService.initTMR(WSDDService.java:253)
	at org.apache.axis.deployment.wsdd.WSDDService.<init>(WSDDService.java:233)
	at 
org.apache.axis.deployment.wsdd.WSDDDeployment.<init>(WSDDDeployment.java:192)
	at 
org.apache.axis.deployment.wsdd.WSDDDocument.setDocument(WSDDDocument.java:139)
	at 
org.apache.axis.deployment.wsdd.WSDDDocument.<init>(WSDDDocument.java:65)
	at 
org.apache.axis.configuration.FileProvider.configureEngine(FileProvider.java:179)
	at org.apache.axis.AxisEngine.init(AxisEngine.java:172)
	at org.apache.axis.AxisEngine.<init>(AxisEngine.java:156)
	at org.apache.axis.server.AxisServer.<init>(AxisServer.java:88)
	at 
org.apache.axis.server.DefaultAxisServerFactory.createServer(DefaultAxisServerFactory.java:109)
	at 
org.apache.axis.server.DefaultAxisServerFactory.getServer(DefaultAxisServerFactory.java:73)
	at org.apache.axis.server.AxisServer.getServer(AxisServer.java:73)
	at 
org.apache.axis.transport.http.AxisServletBase.getEngine(AxisServletBase.java:185)
	at 
org.apache.axis.transport.http.AxisServletBase.getOption(AxisServletBase.java:396)
	at 
org.apache.axis.transport.http.AxisServletBase.init(AxisServletBase.java:112)
	at org.apache.axis.transport.http.AxisServlet.init(AxisServlet.java:156)
	at javax.servlet.GenericServlet.init(GenericServlet.java:212)
	at 
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139)
	at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
	at 
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956)
	at 
org.apache.catalina.core.StandardContext.start(StandardContext.java:4230)
	at 
org.apache.catalina.manager.ManagerServlet.start(ManagerServlet.java:1176)
	at 
org.apache.catalina.manager.HTMLManagerServlet.start(HTMLManagerServlet.java:542)
	at 
org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:105)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
	at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
	at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210)
	at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174)
	at 
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525)
	at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
	at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
	at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
	at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151)
	at 
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870)
	at 
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
	at 
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
	at 
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
	at 
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685)

Re: [Opaltoolkit-users] Problem reloading opal

[Luca C. <lcl...@uc...>]

Anthony Bretaudeau wrote:
> Hi,
> Now that I use the stop opal webapp, wait a minute and then restart it I
> no longer have this HSQLDB problem (although I still get this when stopping:
> Exception in thread "HSQLDB Timer @4e8890da" java.lang.NullPointerException
>     at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
>     at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
>     at java.lang.Thread.run(Thread.java:595)
> )
> 

Anthony,
you can ignore this error.

> However, I still have a problem: services are usually not accessible
> after restarting. I get this kind of error message from clients:
> 

There is a problem in your configuration, but this is a very generic 
error message.


What kind of jobmanager are you using?
Can you try to issue one last, ant clean, ant install?

Can you send me the $CATALINA_HOME/logs/catalina.out?


Sincerely,
Luca


> Exception in thread "main" AxisFault
>  faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
>  faultSubcode:
>  faultString: java.lang.reflect.InvocationTargetException
>  faultActor:
>  faultNode:
>  faultDetail:
>     {http://xml.apache.org/axis/}hostname:genoweb3
> 
> java.lang.reflect.InvocationTargetException
>     at
> org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:221)
>     at
> org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:128)
>     at
> org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087)
>     at
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:604)
>     at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1750)
>     at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2906)
>     at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:624)
>     at
> com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:116)
>     at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:486)
>     at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:810)
>     at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:740)
>     at
> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:110)
>     at
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1208)
>     at
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:525)
>     at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
>     at
> org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227)
>     at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
>     at org.apache.axis.Message.getSOAPEnvelope(Message.java:424)
>     at
> org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62)
>     at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
>     at org.apache.axis.client.Call.invokeEngine(Call.java:2765)
>     at org.apache.axis.client.Call.invoke(Call.java:2748)
>     at org.apache.axis.client.Call.invoke(Call.java:2424)
>     at org.apache.axis.client.Call.invoke(Call.java:2347)
>     at org.apache.axis.client.Call.invoke(Call.java:1804)
>     at
> edu.sdsc.nbcr.opal.AppServicePortTypeSoapBindingStub.launchJob(AppServicePortTypeSoapBindingStub.java:551)
>     at
> CustomOpalClient.CustomOpalClient.launchJob(CustomOpalClient.java:397)
>     at Test.main(Test.java:49)
> 
> It seems like a server problem, maybe with axis? Is this a known
> problem? Is there a solution (apart from restarting tomcat server)?
> Thanks!
> 
> Luca Clementi a écrit :
>> Anthony Bretaudeau wrote:
>>> Hi,
>>> I've got a problem when reloading opal2 app from tomcat manager. After
>>> doing so, registered webservices stop working and the only solution is
>>> to restart tomcat (which is quite uncomfortable as we have other apps in
>>> production on the same tomcat server).
>>> Looking at the log, I see some db related errors when reloading: see
>>> below.
>>> Can you help me?
>>> Thanks!
>> Anthony,
>> we already saw this problem.
>> It is caused by a a race condition of HSQL during the reload of the
>> webapp, basically HSQL is restarted before the old HSQL is completely
>> destroyed. It doesn't always happen, sometime the reload works well.
>>
>> If you use external database this problem won't appear.
>>
>> My suggestion is to stop the webapp, wait some seconds and then start
>> the webapp again, this should avoid this race condition.
>>
>> Sincerely,
>> Luca
>>
>>

Re: [Opaltoolkit-users] Problem reloading opal

[Anthony B. <ant...@ir...>]

Hi,
We're using edu.sdsc.nbcr.opal.manager.DRMAAJobManager (slightly 
modified to work with DRMAA.jar 6.1, but the changes are minor).
Issuing ant clean and ant install didn't solved the problem.
Here's a full log of a tomcat session with the following actions: 
started tomcat, launched a job (which worked), stopped opal2, wait, 
restarted opal2, launched a job

Jul 2, 2009 1:05:03 PM org.apache.catalina.core.AprLifecycleListener 
lifecycleEvent         <------- starting tomcat
INFO: The Apache Tomcat Native library which allows optimal performance 
in production environments was not found on the java.library.path: 
/softs/local/java/jdk1.5.0_12/jre/lib/amd64/server:/softs/local/java/jdk1.5.0_12/jre/lib/amd64:/softs/local/java/jdk1.5.0_12/jre/../lib/amd64:/usr/local/sge/lib/lx24-amd64:/usr/local/sge/lib/lx24-amd64
Jul 2, 2009 1:05:03 PM org.apache.coyote.http11.Http11BaseProtocol init
INFO: Initializing Coyote HTTP/1.1 on http-8383
Jul 2, 2009 1:05:03 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 372 ms
Jul 2, 2009 1:05:03 PM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Jul 2, 2009 1:05:03 PM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/5.5.27
Jul 2, 2009 1:05:03 PM org.apache.catalina.core.StandardHost start
INFO: XML validation disabled
Jul 2, 2009 1:05:03 PM org.apache.catalina.loader.WebappClassLoader 
validateJarFile
init server...
*******engineType:0
*******engineType:0
*******engineType:0
Jul 2, 2009 1:05:15 PM org.apache.coyote.http11.Http11BaseProtocol start
INFO: Starting Coyote HTTP/1.1 on http-8383
Jul 2, 2009 1:05:15 PM org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
Jul 2, 2009 1:05:15 PM org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/12  config=null
Jul 2, 2009 1:05:15 PM org.apache.catalina.storeconfig.StoreLoader load
INFO: Find registry server-registry.xml at classpath resource
Jul 2, 2009 1:05:15 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 12435 ms
[http-8383-Processor23] ERROR manager.DRMAAJobManager  - Can't set hard 
limit - The hardRunDurationLimit attribute is not supported.     <---- 
this is a successfull job launching
Exception in thread "HSQLDB Timer @609a18a0" 
java.lang.NullPointerException      <----- this is when I "Stop" opal2
    at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
    at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
    at java.lang.Thread.run(Thread.java:595)
                                                     <----- Here I 
"Start" opal2 after a moment (no log) and I launch a job (no log here 
but a SOAP fault received by clients)

Luca Clementi a écrit :
> Anthony Bretaudeau wrote:
>> Hi,
>> Now that I use the stop opal webapp, wait a minute and then restart it I
>> no longer have this HSQLDB problem (although I still get this when 
>> stopping:
>> Exception in thread "HSQLDB Timer @4e8890da" 
>> java.lang.NullPointerException
>>     at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
>>     at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
>>     at java.lang.Thread.run(Thread.java:595)
>> )
>>
>
> Anthony,
> you can ignore this error.
>
>> However, I still have a problem: services are usually not accessible
>> after restarting. I get this kind of error message from clients:
>>
>
> There is a problem in your configuration, but this is a very generic 
> error message.
>
>
> What kind of jobmanager are you using?
> Can you try to issue one last, ant clean, ant install?
>
> Can you send me the $CATALINA_HOME/logs/catalina.out?
>
>
> Sincerely,
> Luca
>
>
>> Exception in thread "main" AxisFault
>>  faultCode: 
>> {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
>>  faultSubcode:
>>  faultString: java.lang.reflect.InvocationTargetException
>>  faultActor:
>>  faultNode:
>>  faultDetail:
>>     {http://xml.apache.org/axis/}hostname:genoweb3
>>
>> java.lang.reflect.InvocationTargetException
>>     at
>> org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:221) 
>>
>>     at
>> org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:128) 
>>
>>     at
>> org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:604) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1750) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2906) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:624) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:116) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:486) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:810) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:740) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:110) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1208) 
>>
>>     at
>> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:525) 
>>
>>     at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
>>     at
>> org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227) 
>>
>>     at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
>>     at org.apache.axis.Message.getSOAPEnvelope(Message.java:424)
>>     at
>> org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62) 
>>
>>     at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
>>     at org.apache.axis.client.Call.invokeEngine(Call.java:2765)
>>     at org.apache.axis.client.Call.invoke(Call.java:2748)
>>     at org.apache.axis.client.Call.invoke(Call.java:2424)
>>     at org.apache.axis.client.Call.invoke(Call.java:2347)
>>     at org.apache.axis.client.Call.invoke(Call.java:1804)
>>     at
>> edu.sdsc.nbcr.opal.AppServicePortTypeSoapBindingStub.launchJob(AppServicePortTypeSoapBindingStub.java:551) 
>>
>>     at
>> CustomOpalClient.CustomOpalClient.launchJob(CustomOpalClient.java:397)
>>     at Test.main(Test.java:49)
>>
>> It seems like a server problem, maybe with axis? Is this a known
>> problem? Is there a solution (apart from restarting tomcat server)?
>> Thanks!
>>
>> Luca Clementi a écrit :
>>> Anthony Bretaudeau wrote:
>>>> Hi,
>>>> I've got a problem when reloading opal2 app from tomcat manager. After
>>>> doing so, registered webservices stop working and the only solution is
>>>> to restart tomcat (which is quite uncomfortable as we have other 
>>>> apps in
>>>> production on the same tomcat server).
>>>> Looking at the log, I see some db related errors when reloading: see
>>>> below.
>>>> Can you help me?
>>>> Thanks!
>>> Anthony,
>>> we already saw this problem.
>>> It is caused by a a race condition of HSQL during the reload of the
>>> webapp, basically HSQL is restarted before the old HSQL is completely
>>> destroyed. It doesn't always happen, sometime the reload works well.
>>>
>>> If you use external database this problem won't appear.
>>>
>>> My suggestion is to stop the webapp, wait some seconds and then start
>>> the webapp again, this should avoid this race condition.
>>>
>>> Sincerely,
>>> Luca
>>>
>>>

Re: [Opaltoolkit-users] problem launching opal jobs

[Malcolm T. <mt...@wu...>]

Olivier,

On Tuesday 30 June 2009 02:01:09 am osallou wrote:
> are you sure your issue is not related to your job submission ?

I'm not.  In fact, I expect that this will likely fail until I figure out a 
proper way to get a different default queue for the opal user under PBS.
I was hoping to get everything else working first, then work out this final 
point.  I was also hoping the error messages would help determine the current 
problem.

I'm planning on increasing the logging level and seeing what happens.

Malcolm

> If drmaa could not load the dynamic library it would appear in catalina
> logs. If not error appear, could be a job submission issue.



-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] Problem reloading opal

[Anthony B. <ant...@ir...>]

Hi,
Now that I use the stop opal webapp, wait a minute and then restart it I 
no longer have this HSQLDB problem (although I still get this when stopping:
Exception in thread "HSQLDB Timer @4e8890da" java.lang.NullPointerException
    at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
    at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
    at java.lang.Thread.run(Thread.java:595)
)

However, I still have a problem: services are usually not accessible 
after restarting. I get this kind of error message from clients:

Exception in thread "main" AxisFault
 faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
 faultSubcode:
 faultString: java.lang.reflect.InvocationTargetException
 faultActor:
 faultNode:
 faultDetail:
    {http://xml.apache.org/axis/}hostname:genoweb3

java.lang.reflect.InvocationTargetException
    at 
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:221)
    at 
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:128)
    at 
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087)
    at 
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:604)
    at 
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1750)
    at 
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2906)
    at 
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:624)
    at 
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:116)
    at 
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:486)
    at 
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:810)
    at 
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:740)
    at 
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:110)
    at 
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1208)
    at 
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:525)
    at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
    at 
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227)
    at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
    at org.apache.axis.Message.getSOAPEnvelope(Message.java:424)
    at 
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62)
    at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
    at org.apache.axis.client.Call.invokeEngine(Call.java:2765)
    at org.apache.axis.client.Call.invoke(Call.java:2748)
    at org.apache.axis.client.Call.invoke(Call.java:2424)
    at org.apache.axis.client.Call.invoke(Call.java:2347)
    at org.apache.axis.client.Call.invoke(Call.java:1804)
    at 
edu.sdsc.nbcr.opal.AppServicePortTypeSoapBindingStub.launchJob(AppServicePortTypeSoapBindingStub.java:551)
    at 
CustomOpalClient.CustomOpalClient.launchJob(CustomOpalClient.java:397)
    at Test.main(Test.java:49)

It seems like a server problem, maybe with axis? Is this a known 
problem? Is there a solution (apart from restarting tomcat server)?
Thanks!

Luca Clementi a écrit :
> Anthony Bretaudeau wrote:
>> Hi,
>> I've got a problem when reloading opal2 app from tomcat manager. After
>> doing so, registered webservices stop working and the only solution is
>> to restart tomcat (which is quite uncomfortable as we have other apps in
>> production on the same tomcat server).
>> Looking at the log, I see some db related errors when reloading: see 
>> below.
>> Can you help me?
>> Thanks!
>
> Anthony,
> we already saw this problem.
> It is caused by a a race condition of HSQL during the reload of the 
> webapp, basically HSQL is restarted before the old HSQL is completely 
> destroyed. It doesn't always happen, sometime the reload works well.
>
> If you use external database this problem won't appear.
>
> My suggestion is to stop the webapp, wait some seconds and then start 
> the webapp again, this should avoid this race condition.
>
> Sincerely,
> Luca
>
>
>>
>> Jun 18, 2009 3:18:48 PM org.apache.catalina.core.StandardContext reload
>> INFO: Reloading this Context has started
>> Exception in thread "HSQLDB Timer @5d802746" 
>> java.lang.NullPointerException
>>     at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
>>     at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
>>     at java.lang.Thread.run(Thread.java:595)
>> [http-8383-Processor19] ERROR hbm2ddl.SchemaUpdate  - could not get
>> database metadata
>> java.sql.SQLException: The database is already in use by another
>> process: org.hsqldb.NIOLockFile@f6fbb688[file
>> =/index/www-tmp/opal/opaldb.lck, exists=true, locked=false, valid=false,
>> fl =null]: java.lang.Exception: checkHeartbeat(): lock file
>> [/index/www-tmp/opal/opaldb.lck] is presumably locked by another 
>> process.
>>     at org.hsqldb.jdbc.jdbcUtil.sqlException(Unknown Source)
>>     at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
>>     at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
>>     at org.hsqldb.jdbcDriver.connect(Unknown Source)
>>     at java.sql.DriverManager.getConnection(DriverManager.java:525)
>>     at java.sql.DriverManager.getConnection(DriverManager.java:140)
>>     at
>> org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133) 
>>
>>     at
>> org.hibernate.tool.hbm2ddl.SuppliedConnectionProviderConnectionHelper.prepare(SuppliedConnectionProviderConnectionHelper.java:51) 
>>
>>     at
>> org.hibernate.tool.hbm2ddl.SchemaUpdate.execute(SchemaUpdate.java:168)
>>     at
>> org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:346) 
>>
>>     at
>> org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1327) 
>>
>>     at
>> edu.sdsc.nbcr.opal.state.HibernateUtil.<clinit>(HibernateUtil.java:48)
>>     at
>> edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:79) 
>>
>>     at
>> edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:103) 
>>
>>     at
>> org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) 
>>
>>     at
>> org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
>>     at
>> org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) 
>>
>>     at
>> org.apache.catalina.core.StandardContext.start(StandardContext.java:4230) 
>>
>>     at
>> org.apache.catalina.core.StandardContext.reload(StandardContext.java:3025) 
>>
>>     at
>> org.apache.catalina.manager.ManagerServlet.reload(ManagerServlet.java:904) 
>>
>>     at
>> org.apache.catalina.manager.HTMLManagerServlet.reload(HTMLManagerServlet.java:495) 
>>
>>     at
>> org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:99) 
>>
>>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:627)
>>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
>>     at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) 
>>
>>     at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) 
>>
>>     at
>> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) 
>>
>>     at
>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) 
>>
>>     at
>> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525) 
>>
>>     at
>> org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:276) 
>>
>>     at
>> org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81) 
>>
>>     at
>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) 
>>
>>     at
>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) 
>>
>>     at
>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) 
>>
>>     at
>> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) 
>>
>>     at
>> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875) 
>>
>>     at
>> org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) 
>>
>>     at
>> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) 
>>
>>     at
>> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) 
>>
>>     at
>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) 
>>
>>     at java.lang.Thread.run(Thread.java:595)
>> [http-8383-Processor19] ERROR hbm2ddl.SchemaUpdate  - could not complete
>> schema update
>> java.sql.SQLException: The database is already in use by another
>> process: org.hsqldb.NIOLockFile@f6fbb688[file
>> =/index/www-tmp/opal/opaldb.lck, exists=true, locked=false, valid=false,
>> fl =null]: java.lang.Exception: checkHeartbeat(): lock file
>> [/index/www-tmp/opal/opaldb.lck] is presumably locked by another 
>> process.
>>     at org.hsqldb.jdbc.jdbcUtil.sqlException(Unknown Source)
>>     at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
>>     at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
>>     at org.hsqldb.jdbcDriver.connect(Unknown Source)
>>     at java.sql.DriverManager.getConnection(DriverManager.java:525)
>>     at java.sql.DriverManager.getConnection(DriverManager.java:140)
>>     at
>> org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133) 
>>
>>     at
>> org.hibernate.tool.hbm2ddl.SuppliedConnectionProviderConnectionHelper.prepare(SuppliedConnectionProviderConnectionHelper.java:51) 
>>
>>     at
>> org.hibernate.tool.hbm2ddl.SchemaUpdate.execute(SchemaUpdate.java:168)
>>     at
>> org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:346) 
>>
>>     at
>> org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1327) 
>>
>>     at
>> edu.sdsc.nbcr.opal.state.HibernateUtil.<clinit>(HibernateUtil.java:48)
>>     at
>> edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:79) 
>>
>>     at
>> edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:103) 
>>
>>     at
>> org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) 
>>
>>     at
>> org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
>>     at
>> org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) 
>>
>>     at
>> org.apache.catalina.core.StandardContext.start(StandardContext.java:4230) 
>>
>>     at
>> org.apache.catalina.core.StandardContext.reload(StandardContext.java:3025) 
>>
>>     at
>> org.apache.catalina.manager.ManagerServlet.reload(ManagerServlet.java:904) 
>>
>>     at
>> org.apache.catalina.manager.HTMLManagerServlet.reload(HTMLManagerServlet.java:495) 
>>
>>     at
>> org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:99) 
>>
>>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:627)
>>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
>>     at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) 
>>
>>     at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) 
>>
>>     at
>> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) 
>>
>>     at
>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) 
>>
>>     at
>> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525) 
>>
>>     at
>> org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:276) 
>>
>>     at
>> org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81) 
>>
>>     at
>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) 
>>
>>     at
>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) 
>>
>>     at
>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) 
>>
>>     at
>> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) 
>>
>>     at
>> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875) 
>>
>>     at
>> org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) 
>>
>>     at
>> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) 
>>
>>     at
>> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) 
>>
>>     at
>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) 
>>
>>     at java.lang.Thread.run(Thread.java:595)
>> [http-8383-Processor19] ERROR util.JDBCExceptionReporter  - The database
>> is already in use by another process:
>> org.hsqldb.NIOLockFile@f6fbb688[file =/index/www-tmp/opal/opaldb.lck,
>> exists=true, locked=false, valid=false, fl =null]: java.lang.Exception:
>> checkHeartbeat(): lock file [/index/www-tmp/opal/opaldb.lck] is
>> presumably locked by another process.
>> org.hibernate.exception.JDBCConnectionException: Cannot open connection
>>     at
>> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:97) 
>>
>>     at
>> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66) 
>>
>>     at
>> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:52) 
>>
>>     at
>> org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:449) 
>>
>>     at
>> org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167) 
>>
>>     at
>> org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedConnectionProxy.java:74) 
>>
>>     at $Proxy3.getMetaData(Unknown Source)
>>     at
>> edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:85) 
>>
>>     at
>> edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:103) 
>>
>>     at
>> org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) 
>>
>>     at
>> org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
>>     at
>> org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) 
>>
>>     at
>> org.apache.catalina.core.StandardContext.start(StandardContext.java:4230) 
>>
>>     at
>> org.apache.catalina.core.StandardContext.reload(StandardContext.java:3025) 
>>
>>     at
>> org.apache.catalina.manager.ManagerServlet.reload(ManagerServlet.java:904) 
>>
>>     at
>> org.apache.catalina.manager.HTMLManagerServlet.reload(HTMLManagerServlet.java:495) 
>>
>>     at
>> org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:99) 
>>
>>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:627)
>>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
>>     at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) 
>>
>>     at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) 
>>
>>     at
>> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) 
>>
>>     at
>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) 
>>
>>     at
>> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525) 
>>
>>     at
>> org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:276) 
>>
>>     at
>> org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81) 
>>
>>     at
>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) 
>>
>>     at
>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) 
>>
>>     at
>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) 
>>
>>     at
>> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) 
>>
>>     at
>> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875) 
>>
>>     at
>> org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) 
>>
>>     at
>> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) 
>>
>>     at
>> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) 
>>
>>     at
>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) 
>>
>>     at java.lang.Thread.run(Thread.java:595)
>> Caused by: java.sql.SQLException: The database is already in use by
>> another process: org.hsqldb.NIOLockFile@f6fbb688[file
>> =/index/www-tmp/opal/opaldb.lck, exists=true, locked=false, valid=false,
>> fl =null]: java.lang.Exception: checkHeartbeat(): lock file
>> [/index/www-tmp/opal/opaldb.lck] is presumably locked by another 
>> process.
>>     at org.hsqldb.jdbc.jdbcUtil.sqlException(Unknown Source)
>>     at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
>>     at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
>>     at org.hsqldb.jdbcDriver.connect(Unknown Source)
>>     at java.sql.DriverManager.getConnection(DriverManager.java:525)
>>     at java.sql.DriverManager.getConnection(DriverManager.java:140)
>>     at
>> org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133) 
>>
>>     at
>> org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:446) 
>>
>>     ... 32 more
>>
>> ------------------------------------------------------------------------------ 
>>
>> Crystal Reports - New Free Runtime and 30 Day Trial
>> Check out the new simplified licensing option that enables unlimited
>> royalty-free distribution of the report engine for externally facing
>> server and web deployment.
>> http://p.sf.net/sfu/businessobjects
>> _______________________________________________
>> Opaltoolkit-users mailing list
>> Opa...@li...
>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>

Re: [Opaltoolkit-users] problem launching opal jobs

[osallou <oli...@ir...>]

Hi,
are you sure your issue is not related to your job submission ?
If drmaa could not load the dynamic library it would appear in catalina 
logs. If not error appear, could be a job submission issue.

Sriram Krishnan a écrit :
>>
>>> Nope, all I'm seeing is:
>>
>> catalina.out:2009-06-26 13:18:12,515 INFO  
>> edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) 
>> - Using
>> job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
>>
>> Is there an easy way for me to test whether the 3rd party package is
>> configured/working properly?
>
> Not that we know of. But we now do have a virtual PBS cluster here. 
> Will let you know how it goes.
>
>> Is there some way for me to increase the verbosity of the debugging?
>
> You can increase the Opal debugging by editing the 
> lib/log4j.properties. You should change the line
> log4j.logger.edu.sdsc=WARN
> to
> log4j.logger.edu.sdsc=DEBUG
>
> After you do this, you will have to shut down tomcat, re-install Opal 
> (ant install) and restart Tomcat. You should get more debug messages 
> from Opal.
>
> Let us know if you see anything interesting with the increased logging 
> information.
>
> Cheers,
> Sriram
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>   

Re: [Opaltoolkit-users] problem launching opal jobs

[Sriram K. <sr...@sd...>]

>
>> Nope, all I'm seeing is:
>
> catalina.out:2009-06-26 13:18:12,515 INFO
> edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579)  
> - Using
> job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
>
> Is there an easy way for me to test whether the 3rd party package is
> configured/working properly?

Not that we know of. But we now do have a virtual PBS cluster here.  
Will let you know how it goes.

> Is there some way for me to increase the verbosity of the debugging?

You can increase the Opal debugging by editing the lib/ 
log4j.properties. You should change the line
log4j.logger.edu.sdsc=WARN
to
log4j.logger.edu.sdsc=DEBUG

After you do this, you will have to shut down tomcat, re-install Opal  
(ant install) and restart Tomcat. You should get more debug messages  
from Opal.

Let us know if you see anything interesting with the increased logging  
information.

Cheers,
Sriram

Re: [Opaltoolkit-users] problem launching opal jobs

[Malcolm T. <mt...@wu...>]

Sriram,

On Monday 29 June 2009 12:44:47 pm Sriram Krishnan wrote:
> Whether it is using DRMAA or not is defined in the opal.properties
> file. You can verify that it is using DRMAA by looking at your Tomcat
> logs. If it is indeed using DRMAA, Opal should print the following to
> the log - "Using job manager class: job manager class being used".

Gotcha.

> Ideally, it should really throw an exception. In fact, most errors are
> indeed logged by Opal/Tomcat. However, the DRMAA support is provided
> by using a 3rd party package that uses the Java Native Interface. We
> have noticed that it sometimes dies silently, rather than throwing a
> useful exception (however, this doesn't happen once DRMAA has been
> properly configured). In any case, do you have a line in your Tomcat
> log like - "Can't initialize DRMAA session:".

Nope, all I'm seeing is:

catalina.out:2009-06-26 13:18:12,515 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) - Using 
job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager

Is there an easy way for me to test whether the 3rd party package is 
configured/working properly?

Is there some way for me to increase the verbosity of the debugging?

Malcolm

-- 
Malcolm Tobias
314.362.1594