opaltoolkit-users — Users mailing-list for Opal Toolkit

Re: [Opaltoolkit-users] problem launching opal jobs

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

>
>>> Maybe it would help if I understood Java better.  If I was  
>>> building a
> Fortran/C program with autoconf, I'd expect to have to pass  
> configure some
> option to use DRMAA.  This would either produce a staticly-linked  
> binary that
> would produce a compile-time error if it couldn't find the library,  
> or a
> dynamically-linked binary that would produce a run-time error if it  
> couldn't
> find the library.

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".

> With Tomcat, I haven't done anything to tell it to use DRMAA.  There  
> doesn't
> seem to be the equivalent of a binary that I could run 'ldd' on to  
> verify it
> was going to use libdrmaa.  Maybe that's because the support for  
> DRMAA is in
> the Opal stuff (e.g. /webapps/opal2/WEB-INF/lib/drmaa.jar)?  How can  
> I debug
> whether Tomcat is failing to find the library?  Why wouldn't Tomcat/ 
> Opal
> complain if it couldn't find libdrmaa rather than fail silently?

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:".

Thanks,
Sriram

Re: [Opaltoolkit-users] problem launching opal jobs

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

Sriram,

On Sunday 28 June 2009 12:59:04 pm Sriram Krishnan wrote:

> > It wasn't clear to me whether this needs to be set when doing the 'ant
> > install' stage, or when starting Tomcat so I did both.  
>
> The Tomcat server is the one that needs the libdrmaa to be in its
> LD_LIBRARY_PATH because it needs to launch the jobs via DRMAA. The
> client doesn't need this property to be set. Make sure that that this
> environment variable is set correctly before starting Tomcat (and also
> that this environment variable is available to Tomcat as well). I am
> assuming that you are starting up Tomcat from a bash shell - so an
> export LD_LIBRARY_PATH before running the Tomcat start script on the
> same shell should do the trick.

I tried to make it clear in my email that a) I had set LD_LIBRARY_PATH b) it 
included libdrmaa (i.e. 'ls $LD_LIBRARY_PATH') and c) I was using the same 
shell to start Tomcat.  Even after that, I'm still seeing the error.

Maybe it would help if I understood Java better.  If I was building a 
Fortran/C program with autoconf, I'd expect to have to pass configure some 
option to use DRMAA.  This would either produce a staticly-linked binary that 
would produce a compile-time error if it couldn't find the library, or a 
dynamically-linked binary that would produce a run-time error if it couldn't 
find the library.

With Tomcat, I haven't done anything to tell it to use DRMAA.  There doesn't 
seem to be the equivalent of a binary that I could run 'ldd' on to verify it 
was going to use libdrmaa.  Maybe that's because the support for DRMAA is in 
the Opal stuff (e.g. /webapps/opal2/WEB-INF/lib/drmaa.jar)?  How can I debug 
whether Tomcat is failing to find the library?  Why wouldn't Tomcat/Opal 
complain if it couldn't find libdrmaa rather than fail silently?

Malcolm

-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Malcolm,

Couple of comments inline -

>>
> It wasn't clear to me whether this needs to be set when doing the 'ant
> install' stage, or when starting Tomcat so I did both.  I started  
> with my
> working configuration with Fork, changed the opal.properties and the  
> job's
> properties to use DRMAA, undeployed and deployed the application and  
> verified
> that in each case I could see the libdrmaa via:
>

The Tomcat server is the one that needs the libdrmaa to be in its  
LD_LIBRARY_PATH because it needs to launch the jobs via DRMAA. The  
client doesn't need this property to be set. Make sure that that this  
environment variable is set correctly before starting Tomcat (and also  
that this environment variable is available to Tomcat as well). I am  
assuming that you are starting up Tomcat from a bash shell - so an  
export LD_LIBRARY_PATH before running the Tomcat start script on the  
same shell should do the trick.

> I'm just taking a WAG here, but the client complains:
>
> faultCode: {http://schemas.xmlsoap.org/soap/ 
> envelope/}Server.userException
>
> and the server complains:
>
> edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's  
> DN: Unknown
> client
> 2009-06-26 13:18:12,508 INFO
> edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's IP:
> 127.0.0.1
>
> This makes me wonder if there is some authentication problem.
>
> Is there a problem if I'm running the client as root?  If I'm  
> running it from
> the same system that the server is running from?

I assure you that this is not a problem. If you were running the  
service via SSL and had set up an authorization handler, the client's  
DN would be used to restrict access to the service. However, since you  
are running this service over regular HTTP, this information is simply  
logged, and no action taken. So there is no authentication issue for  
sure.

We are running some tests here to test out Opal with DRMAA+PBS - will  
let you know how that goes. Thanks for testing this feature out for us.

Cheers,
Sriram

Re: [Opaltoolkit-users] problem launching opal jobs

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

Luca,

On Thursday 25 June 2009 03:30:36 pm Luca Clementi wrote:
> but if you use fork, Opal will simply fork the job on the node where the
> tomcat is running.
>
> The problem you are experiencing is connected with the libdrmaa.so so if
> you use fork everything is fine.

I understand that, but given that the DRMAA stuff wasn't working correctly, it 
was nice to back off to a simpler setup and verify that that was indeed 
working before continuing to the more complicated setup.

> To update the LD_LIBRARY_PATH try running
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<your path to libdrmaa.so>

It wasn't clear to me whether this needs to be set when doing the 'ant 
install' stage, or when starting Tomcat so I did both.  I started with my 
working configuration with Fork, changed the opal.properties and the job's 
properties to use DRMAA, undeployed and deployed the application and verified 
that in each case I could see the libdrmaa via:

-bash-3.1$ ls $LD_LIBRARY_PATH
libattr.a    libdrmaa.so.0      libsite.a       libtorque.so.0.0.0
libcmds.a    libdrmaa.so.0.0.0  libtorque.a     libtorque.so.2
libdrmaa.a   liblog.a           libtorque.la    libtorque.so.2.0.0
libdrmaa.la  libnet.a           libtorque.so    pbs_sched.a
libdrmaa.so  libpbs.a           libtorque.so.0

I did this before executing any commands.

Here's what I see when I try to submit a job:

[root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave.wustl.edu:8080/opal2/services/pdb2pqr -r 
launchJob -a "--ff=amber sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://agave.wustl.edu:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
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:agave.wustl.edu

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 org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown 
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
        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 
edu.sdsc.nbcr.opal.GenericServiceClient.main(GenericServiceClient.java:311)

and from the Tomcat logs:

2009-06-26 13:18:12,492 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchJob(AppServiceImpl.java:237) - called
2009-06-26 13:18:12,494 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java:1038) - 
called
2009-06-26 13:18:12,500 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java:944) - 
called
2009-06-26 13:18:12,506 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's DN: Unknown 
client
2009-06-26 13:18:12,508 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's IP: 
127.0.0.1
2009-06-26 13:18:12,509 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java:72) - 
called
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


I'm just taking a WAG here, but the client complains:

 faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException

and the server complains:

edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's DN: Unknown 
client
2009-06-26 13:18:12,508 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's IP: 
127.0.0.1

This makes me wonder if there is some authentication problem.

Is there a problem if I'm running the client as root?  If I'm running it from 
the same system that the server is running from?  

Malcolm




-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Malcolm Tobias wrote:
> Wilfred,
> 
> On Thursday 25 June 2009 11:34:03 am Wilfred Li wrote:
>> Looking at your opal.properties file, I'd suggest that you use the
>> ForkJobManager for now to debug your installation, since we haven't figured
>> out how to configure the DRMAAJobManager with PBS yet. We used PBS 4 or 5
>> years ago, but switched to SGE for a number of reasons. You can do this by
>> adding the appConfig entry
>>
>> <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>,
>> or edit your current entry for DRMAAJobmanager.
> 
> This seems like a good suggestion.  I tried using ForkJobManager and it 
> worked!
> 
> [root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
> http://agave.wustl.edu:8080/opal2/services/pdb2pqr -r 
> launchJob -a "--ff=amber sample.pdb output.pqr" -f samples/sample.pdb
> 
> Reading command line arguments
> Service URL: http://agave.wustl.edu:8080/opal2/services/pdb2pqr
> Invoking operation: launchJob
> 
> Command line arguments: --ff=amber sample.pdb output.pqr
> Making non-blocking invocation on Opal service -
> Received jobID: app1245958071884
> Current Status:
>         Code: 1
>         Message: Launching executable
>         Output Base URL: http://agave.wustl.edu:8080/app1245958071884
> 
> I'll try to focus on making sure that the user running opal can access the 
> correct queues by default.  
> 
> Malcolm
> 

Malcom,
but if you use fork, Opal will simply fork the job on the node where the 
tomcat is running.

The problem you are experiencing is connected with the libdrmaa.so so if 
you use fork everything is fine.

To update the LD_LIBRARY_PATH try running
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<your path to libdrmaa.so>

Sincerely,
Luca

Re: [Opaltoolkit-users] problem launching opal jobs

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

Wilfred,

On Thursday 25 June 2009 11:34:03 am Wilfred Li wrote:
> Looking at your opal.properties file, I'd suggest that you use the
> ForkJobManager for now to debug your installation, since we haven't figured
> out how to configure the DRMAAJobManager with PBS yet. We used PBS 4 or 5
> years ago, but switched to SGE for a number of reasons. You can do this by
> adding the appConfig entry
>
> <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>,
> or edit your current entry for DRMAAJobmanager.

This seems like a good suggestion.  I tried using ForkJobManager and it 
worked!

[root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave.wustl.edu:8080/opal2/services/pdb2pqr -r 
launchJob -a "--ff=amber sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://agave.wustl.edu:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
Received jobID: app1245958071884
Current Status:
        Code: 1
        Message: Launching executable
        Output Base URL: http://agave.wustl.edu:8080/app1245958071884

I'll try to focus on making sure that the user running opal can access the 
correct queues by default.  

Malcolm



-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Luca,

On Thursday 25 June 2009 12:24:21 pm Luca Clementi wrote:

> The problem you are experiencing is due to the fact that you don't have
> available the libdrmaa.so on your LD_LIBRARY_PATH. This library should
> be shipped with your scheduler.
>
> Please check that
> echo $LD_LIBRARY_PATH
> points to the base directory where you have your libdrmaa.so. If not you
> have to add the path to you LD_LIBRARY_PATH and restart tomcat.

It wasn't clear to me at what point this had to be set.  Is it during the 'ant 
install' phase, or when I start Tomcat (I did this as 2 different users).  
Since I didn't see any complaints about missing symbols, I had assumed 
everything is OK.

I stopped tomcat, made sure that LD_LIBRARY_PATH has libdrmma in it's path, 
and restarted tomcat:

-bash-3.1$ ls $LD_LIBRARY_PATH
libattr.a    libdrmaa.so.0      libsite.a       libtorque.so.0.0.0
libcmds.a    libdrmaa.so.0.0.0  libtorque.a     libtorque.so.2
libdrmaa.a   liblog.a           libtorque.la    libtorque.so.2.0.0
libdrmaa.la  libnet.a           libtorque.so    pbs_sched.a
libdrmaa.so  libpbs.a           libtorque.so.0

-bash-3.1$ /usr/local/src/jakarta-tomcat-5.0.30/bin/startup.sh 

I'm still seeing the same error when I try to submit a job from the client.

> I'm not an expert of torque but taking a look at the documentation it
> seems that you have to use routing queue to specify the default queue
> for the opaluser.
>
> Please have a look at
> http://www.clusterresources.com/torquedocs21/4.1queueconfig.shtml
> You should route all the job to
> opal_queue first and then to all the other queues. Then opal_queue
> should have the acl_users enabled only for opaluser.

This sounds like it might work.  I currently have a couple of queues set up, 
and I wanted to make sure that the existing way people submit jobs continue 
to work.  

Malcolm


-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Malcolm Tobias wrote:
> Luca,
> 
> On Thursday 25 June 2009 11:59:50 am you wrote:
>> can you send me the $CATALINA_HOME/logs/catalina.out ?
> 
> I've attached it.
> 
>> To further debug your problem with torque, would it be possible to have
>> an account on agave?
> 
> I'll have to look into getting the PI's permission.
> 
> Cheers,
> Malcolm
> 
> 

Malcom,
The problem you are experiencing is due to the fact that you don't have 
available the libdrmaa.so on your LD_LIBRARY_PATH. This library should 
be shipped with your scheduler.

Please check that
echo $LD_LIBRARY_PATH
points to the base directory where you have your libdrmaa.so. If not you 
have to add the path to you LD_LIBRARY_PATH and restart tomcat.

I'm not an expert of torque but taking a look at the documentation it 
seems that you have to use routing queue to specify the default queue 
for the opaluser.

Please have a look at 
http://www.clusterresources.com/torquedocs21/4.1queueconfig.shtml
You should route all the job to
opal_queue first and then to all the other queues. Then opal_queue 
should have the acl_users enabled only for opaluser.



Sincerely,
Luca

Re: [Opaltoolkit-users] problem launching opal jobs

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

Wilfred,

On Thursday 25 June 2009 11:40:51 am Wilfred Li wrote:
> What version of PBS are you using, and what is the OS for the cluster?
> We'll try to find something similar or set up a virtual cluster to check
> out this issue with PBS.

I recently upgrade to torque-2.3.6.  This is one of the many variants of PBS.
I verified that it had DRMAA support.  The OS is Fedora Core 6.  The hardware 
is pretty ancient and more recent OSs had problems.

Malcolm

-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Hi, Malcolm,

What version of PBS are you using, and what is the OS for the cluster?
We'll try to find something similar or set up a virtual cluster to check
out this issue with PBS.

Cheers,

Wilfred


-----Original Message-----
From: Malcolm Tobias [mailto:mt...@wu...] 
Sent: Tuesday, June 23, 2009 12:28 PM
To: opa...@li...
Subject: [Opaltoolkit-users] problem launching opal jobs


I'm attempting to set up our own local pdb2pqr Opal server following the
instructions at:

http://www.nbcr.net/software/opal/docs/2.0/installation.html

After customizing the XML configuration to point to our local pdb2pqr, I

deployed the service:

ant deploy -DserviceName=pdb2pqr -DappConfig=./pdb2pqr_config.xml 

I then tried to use the client to launch a job:

java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://agave:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
Exception in thread "main" AxisFault
 faultCode:
{http://schemas.xmlsoap.org/soap/envelope/}Server.generalException
 faultSubcode: 
 faultString: 
 faultActor: 
 faultNode: 
 faultDetail: 
        {http://nbcr.sdsc.edu/opal/types}opalFaultOutput:<message>Can't 
instantiate Opal Job Manager - Job manager class 
edu.sdsc.ncbr.opal.manager.DRMAAJobManager not found</message>
        
{http://xml.apache.org/axis/}exceptionName:edu.sdsc.nbcr.opal.FaultType
        {http://xml.apache.org/axis/}hostname:agave.wustl.edu

The job manager that I have specified in my pdb2pqr_config.xml file is:

<jobManagerFQCN>edu.sdsc.ncbr.opal.manager.DRMAAJobManager</jobManagerFQ
CN>

The corresponding job manager defined in my etc/opal.properties is:

   opal.jobmanager=edu.sdsc.ncbr.opal.manager.DRMAAJobManager

Any ideas on what might be wrong?


A second question that I'll need to address at some point is how to
customize 
the batch script that is used for launching the jobs.  We have an
existing 
cluster (running PBS/torque) and I'd like to define a property that
denotes 
that some special nodes are available for running Opal jobs.  If I were
doing 
this manually, instead of specifying:

qsub -I -lnodes=1

I'd do this by specifying:

qsub -I -lnodes=1:opal

Is there some way to customize how Opal talking to the queuing system
via 
DRMAA?

Thanks,
Malcolm


-- 
Malcolm Tobias
314.362.1594


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Re: [Opaltoolkit-users] problem launching opal jobs

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

Looking at your opal.properties file, I'd suggest that you use the ForkJobManager for now to debug your installation, since we haven't figured out how to configure the DRMAAJobManager with PBS yet. We used PBS 4 or 5 years ago, but switched to SGE for a number of reasons. You can do this by adding the appConfig entry 

<jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>, or edit your current entry for DRMAAJobmanager. 

I've attached the pdb2pqr appConfig file that we have. I suspect that with Opal 2.0, the application version number is supposed to be part of the URL. That's explicitly specified in the appConfig file. But Luca can clarify on that.

Our plan is to include the appConfig files that we use as a template in future distributions of Opal.

Cheers,

Wilfred


-----Original Message-----
From: Malcolm Tobias [mailto:mt...@wu...] 
Sent: Thursday, June 25, 2009 9:07 AM
To: Wilfred Li
Cc: opa...@li...
Subject: Re: [Opaltoolkit-users] problem launching opal jobs


Wilfred,

On Thursday 25 June 2009 10:30:45 am Wilfred Li wrote:
> I got the same error when I tried your service using the Opal Client, 
> whereas the ws.nbcr.net pdb2pqr service returned a successful launch. 
> My guess is still an configuration issue. Could you please send me 
> your opal.properties file and your app config file for pdb2pqr?

Sure.  They're attached.

> [wilfred@rocks-32 opal-ws-2.0]$ java
> edu.sdsc.nbcr.opal.GenericServiceClient -l 
> http://ws.nbcr.net/opal2/services/pdb2pqr_1.4.0 -r launchJob -a 
> "--ff=amber sample.pdb output.pqr" -f samples/sample.pdb

FWIW, I verified I could also use your server, which I guess rules out problems with my client.

I should mention that I do expect jobs to fail at some point with our server.
The user running Tomcat doesn't have permission to run jobs on the default queue.  I'm still trying to figure out how to have a different default queue for this specific user.  Luca mentioned that you use .sge_request for SGE but I can't find any equivalent configuration file for PBS.  I'm guessing the server would tell the client that it has accepted the job, and then it would fail to run.  I'm not sure if that is responsible for the current error.  

Malcolm

--
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Wilfred,

On Thursday 25 June 2009 10:30:45 am Wilfred Li wrote:
> I got the same error when I tried your service using the Opal Client,
> whereas the ws.nbcr.net pdb2pqr service returned a successful launch. My
> guess is still an configuration issue. Could you please send me your
> opal.properties file and your app config file for pdb2pqr?

Sure.  They're attached.

> [wilfred@rocks-32 opal-ws-2.0]$ java
> edu.sdsc.nbcr.opal.GenericServiceClient -l
> http://ws.nbcr.net/opal2/services/pdb2pqr_1.4.0 -r launchJob -a "--ff=amber
> sample.pdb output.pqr" -f samples/sample.pdb

FWIW, I verified I could also use your server, which I guess rules out 
problems with my client.

I should mention that I do expect jobs to fail at some point with our server.
The user running Tomcat doesn't have permission to run jobs on the default 
queue.  I'm still trying to figure out how to have a different default queue 
for this specific user.  Luca mentioned that you use .sge_request for SGE but 
I can't find any equivalent configuration file for PBS.  I'm guessing the 
server would tell the client that it has accepted the job, and then it would 
fail to run.  I'm not sure if that is responsible for the current error.  

Malcolm

-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

I got the same error when I tried your service using the Opal Client, whereas the ws.nbcr.net pdb2pqr service returned a successful launch. My guess is still an configuration issue. Could you please send me your opal.properties file and your app config file for pdb2pqr? 

[wilfred@rocks-32 opal-ws-2.0]$ java edu.sdsc.nbcr.opal.GenericServiceClient -l http://ws.nbcr.net/opal2/services/pdb2pqr_1.4.0 -r launchJob -a "--ff=amber sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://ws.nbcr.net/opal2/services/pdb2pqr_1.4.0
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
Received jobID: app1245943395564
Current Status:
	Code: 1
	Message: Launching executable
	Output Base URL: http://ws.nbcr.net/app1245943395564

Cheers,

Wilfred

-----Original Message-----
From: Malcolm Tobias [mailto:mt...@wu...] 
Sent: Thursday, June 25, 2009 7:10 AM
To: Wilfred Li
Cc: opa...@li...
Subject: Re: [Opaltoolkit-users] problem launching opal jobs


Wilfred,

On Thursday 25 June 2009 09:04:04 am Wilfred Li wrote:
> Could you try using the FQDN of agave on your command line?

I get the same error.  FWIW, I'm running the client and server on the same 
system:

[root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave.wustl.edu:8080/opal2/services/pdb2pqr -r 
launchJob -a "--ff=amber sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://agave.wustl.edu:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
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:agave.wustl.edu

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 org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown 
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
        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 
edu.sdsc.nbcr.opal.GenericServiceClient.main(GenericServiceClient.java:311)

Here are the contents of the Tomcat log if that helps:

2009-06-25 09:06:33,177 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchJob(AppServiceImpl.java:237) - called
2009-06-25 09:06:33,182 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java:1038) - 
called
2009-06-25 09:06:33,184 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java:944) - 
called
2009-06-25 09:06:33,194 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's DN: Unknown 
client
2009-06-25 09:06:33,203 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's IP: 
127.0.0.1
2009-06-25 09:06:33,204 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java:72) - 
called
2009-06-25 09:06:33,216 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) - Using 
job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager

Is the message: "Client's DN: Unknown client" relevant?


Malcolm




-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Could you try using the FQDN of agave on your command line?

Best regards,

Wilfred

Sent from my FUZE™

-----Original Message-----
From: Malcolm Tobias <mt...@wu...>
Sent: 2009年6月25日 上午 06:03
To: Luca Clementi <lcl...@uc...>
Cc: opa...@li... <opa...@li...>
Subject: Re: [Opaltoolkit-users] problem launching opal jobs


Luca,

On Wednesday 24 June 2009 03:40:18 pm Luca Clementi wrote:
> there is a space between the . and etc/classpath.sh
> . etc/classpath.sh
> if you write ./etc/classpath.sh it is going to work.
>
> I guess that if you properly load the classpath.sh the errors should
> disapear.

Even with the CLASSPATH set:

[root@agave opal-ws-2.0]# printenv | grep CLASS
CLASSPATH=/usr/local/src/opal-ws-2.0:/usr/local/src/opal-ws-2.0/build/classes:/usr/local/src/opal-ws-2.0/lib:/usr/local/src/opal-ws-2.0/etc:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/axis-ant.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/axis.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/commons-discovery-0.2.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/commons-logging-1.0.4.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/jaxrpc.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/saaj.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/wsdl4j-1.5.1.jar:/usr/local/src/opal-ws-2.0/lib/activation-1_0_2.jar:/usr/local/src/opal-ws-2.0/lib/antlr-2.7.6.jar:/usr/local/src/opal-ws-2.0/lib/cglib-2.1.3.jar:/usr/local/src/opal-ws-2.0/lib/cog-axis.jar:/usr/local/src/opal-ws-2.0/lib/cog-jglobus.jar:/usr/local/src/opal-ws-2.0/lib/cog-tomcat.jar:/usr/local/src/opal-ws-2.0/lib/cog-url.jar:/usr/local/src/opal-ws-2.0/lib/commons-cl!
 i-2.0.jar:/usr/local/src/opal-ws-2.0/lib/commons-collections-3.1.jar:/usr/local/src/opal-ws-2.0/lib/cryptix32.jar:/usr/local/src/opal-ws-2.0/lib/cryptix-asn1.jar:/usr/local/src/opal-ws-2.0/lib/cryptix.jar:/usr/local/src/opal-ws-2.0/lib/dom4j-1.6.1.jar:/usr/local/src/opal-ws-2.0/lib/drmaa.jar:/usr/local/src/opal-ws-2.0/lib/hibernate3.jar:/usr/local/src/opal-ws-2.0/lib/hsqldb.jar:/usr/local/src/opal-ws-2.0/lib/javassist-3.4.GA.jar:/usr/local/src/opal-ws-2.0/lib/jce-jdk13-125.jar:/usr/local/src/opal-ws-2.0/lib/jcommon-1.0.12.jar:/usr/local/src/opal-ws-2.0/lib/jdom-1.1.jar:/usr/local/src/opal-ws-2.0/lib/jfreechart-1.0.8.jar:/usr/local/src/opal-ws-2.0/lib/jgss.jar:/usr/local/src/opal-ws-2.0/lib/jta-1.1.jar:/usr/local/src/opal-ws-2.0/lib/junit-4.4.jar:/usr/local/src/opal-ws-2.0/lib/log4j-1.2.15.jar:/usr/local/src/opal-ws-2.0/lib/mailapi-1_3_1.jar:/usr/local/src/opal-ws-2.0/lib/postgresql-8.2-506.jdbc3.jar:/usr/local/src/opal-ws-2.0/lib/puretls.jar:/usr/local/src/opal-ws-2.0/lib/r!
 ome-1.0RC1.jar:/usr/local/src/opal-ws-2.0/lib/servlet-api-2_4.jar:/usr
/local/src/opal-ws-2.0/lib/slf4j-api-1.5.2.jar:/usr/local/src/opal-ws-2.0/lib/slf4j-log4j12-1.5.2.jar:/usr/local/src/opal-ws-2.0/lib/xercesImpl.jar

I'm getting the error:

[root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://agave:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
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:agave.wustl.edu

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 org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown 
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
        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 
edu.sdsc.nbcr.opal.GenericServiceClient.main(GenericServiceClient.java:311)

Malcolm


-- 
Malcolm Tobias
314.362.1594


------------------------------------------------------------------------------
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Opaltoolkit-users mailing list
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https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

Re: [Opaltoolkit-users] problem launching opal jobs

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

Wilfred,

On Thursday 25 June 2009 09:04:04 am Wilfred Li wrote:
> Could you try using the FQDN of agave on your command line?

I get the same error.  FWIW, I'm running the client and server on the same 
system:

[root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave.wustl.edu:8080/opal2/services/pdb2pqr -r 
launchJob -a "--ff=amber sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://agave.wustl.edu:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
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:agave.wustl.edu

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 org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown 
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
        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 
edu.sdsc.nbcr.opal.GenericServiceClient.main(GenericServiceClient.java:311)

Here are the contents of the Tomcat log if that helps:

2009-06-25 09:06:33,177 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchJob(AppServiceImpl.java:237) - called
2009-06-25 09:06:33,182 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java:1038) - 
called
2009-06-25 09:06:33,184 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java:944) - 
called
2009-06-25 09:06:33,194 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's DN: Unknown 
client
2009-06-25 09:06:33,203 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's IP: 
127.0.0.1
2009-06-25 09:06:33,204 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java:72) - 
called
2009-06-25 09:06:33,216 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) - Using 
job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager

Is the message: "Client's DN: Unknown client" relevant?


Malcolm




-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Luca,

On Wednesday 24 June 2009 03:40:18 pm Luca Clementi wrote:
> there is a space between the . and etc/classpath.sh
> . etc/classpath.sh
> if you write ./etc/classpath.sh it is going to work.
>
> I guess that if you properly load the classpath.sh the errors should
> disapear.

Even with the CLASSPATH set:

[root@agave opal-ws-2.0]# printenv | grep CLASS
CLASSPATH=/usr/local/src/opal-ws-2.0:/usr/local/src/opal-ws-2.0/build/classes:/usr/local/src/opal-ws-2.0/lib:/usr/local/src/opal-ws-2.0/etc:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/axis-ant.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/axis.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/commons-discovery-0.2.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/commons-logging-1.0.4.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/jaxrpc.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/saaj.jar:/usr/local/src/opal-ws-2.0/webapps/opal2/WEB-INF/lib/wsdl4j-1.5.1.jar:/usr/local/src/opal-ws-2.0/lib/activation-1_0_2.jar:/usr/local/src/opal-ws-2.0/lib/antlr-2.7.6.jar:/usr/local/src/opal-ws-2.0/lib/cglib-2.1.3.jar:/usr/local/src/opal-ws-2.0/lib/cog-axis.jar:/usr/local/src/opal-ws-2.0/lib/cog-jglobus.jar:/usr/local/src/opal-ws-2.0/lib/cog-tomcat.jar:/usr/local/src/opal-ws-2.0/lib/cog-url.jar:/usr/local/src/opal-ws-2.0/lib/commons-cli-2.0.jar:/usr/local/src/opal-ws-2.0/lib/commons-collections-3.1.jar:/usr/local/src/opal-ws-2.0/lib/cryptix32.jar:/usr/local/src/opal-ws-2.0/lib/cryptix-asn1.jar:/usr/local/src/opal-ws-2.0/lib/cryptix.jar:/usr/local/src/opal-ws-2.0/lib/dom4j-1.6.1.jar:/usr/local/src/opal-ws-2.0/lib/drmaa.jar:/usr/local/src/opal-ws-2.0/lib/hibernate3.jar:/usr/local/src/opal-ws-2.0/lib/hsqldb.jar:/usr/local/src/opal-ws-2.0/lib/javassist-3.4.GA.jar:/usr/local/src/opal-ws-2.0/lib/jce-jdk13-125.jar:/usr/local/src/opal-ws-2.0/lib/jcommon-1.0.12.jar:/usr/local/src/opal-ws-2.0/lib/jdom-1.1.jar:/usr/local/src/opal-ws-2.0/lib/jfreechart-1.0.8.jar:/usr/local/src/opal-ws-2.0/lib/jgss.jar:/usr/local/src/opal-ws-2.0/lib/jta-1.1.jar:/usr/local/src/opal-ws-2.0/lib/junit-4.4.jar:/usr/local/src/opal-ws-2.0/lib/log4j-1.2.15.jar:/usr/local/src/opal-ws-2.0/lib/mailapi-1_3_1.jar:/usr/local/src/opal-ws-2.0/lib/postgresql-8.2-506.jdbc3.jar:/usr/local/src/opal-ws-2.0/lib/puretls.jar:/usr/local/src/opal-ws-2.0/lib/rome-1.0RC1.jar:/usr/local/src/opal-ws-2.0/lib/servlet-api-2_4.jar:/usr/local/src/opal-ws-2.0/lib/slf4j-api-1.5.2.jar:/usr/local/src/opal-ws-2.0/lib/slf4j-log4j12-1.5.2.jar:/usr/local/src/opal-ws-2.0/lib/xercesImpl.jar

I'm getting the error:

[root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://agave:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
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:agave.wustl.edu

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 org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown 
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
        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 
edu.sdsc.nbcr.opal.GenericServiceClient.main(GenericServiceClient.java:311)

Malcolm


-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Malcolm Tobias wrote:
> Luca,
> 
> On Wednesday 24 June 2009 01:02:42 pm Luca Clementi wrote:
>>> After fixing it, I'm getting a different error when I try to submit a
>>> job:
>>>
>>> [root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l
>>> http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber
>>> sample.pdb output.pqr" -f samples/sample.pdb
>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>> edu/sdsc/nbcr/opal/GenericServiceClient
>>> Caused by: java.lang.ClassNotFoundException:
>>> edu.sdsc.nbcr.opal.GenericServiceClient
>>>         at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
>>>         at java.security.AccessController.doPrivileged(Native Method)
>>>         at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>>>         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>>>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>>>         at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
>>>         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
>>> Could not find the main class: edu.sdsc.nbcr.opal.GenericServiceClient.  
>>> Program will exit.
>> Tobias,
>> you have to set the classpath properly before you can use the Opal
>> client. Please run
>> . etc/classpath.sh
>> if you are using bash.
> 
> I thought running the shell script would set the CLASSPATH, but for some weird 
> reason it doesn't.  It just prints out the list of directories:
> 
> [root@agave opal-ws-2.0]# ./etc/classpath.sh 
> 

Tobias,
there is a space between the . and etc/classpath.sh
. etc/classpath.sh
if you write ./etc/classpath.sh it is going to work.

I guess that if you properly load the classpath.sh the errors should 
disapear.


Sincerely,
Luca

> [root@agave opal-ws-2.0]# echo $CLASSPATH
> 
> [root@agave opal-ws-2.0]# printenv | grep CLASS
> [root@agave opal-ws-2.0]# 
> 
> It probably doesn't matter why it's failing.  I manually set it.
> Here's what I see now:
> 
> [root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
> http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
> sample.pdb output.pqr" -f samples/sample.pdb
> 
> Reading command line arguments
> Service URL: http://agave:8080/opal2/services/pdb2pqr
> Invoking operation: launchJob
> 
> Command line arguments: --ff=amber sample.pdb output.pqr
> Making non-blocking invocation on Opal service -
> Exception in thread "main" AxisFault
>  faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
>  faultSubcode: 
>  faultString: java.lang.reflect.InvocationTargetException
>  faultActor: 
>  faultNode: 
>  faultDetail: 
>         {http://xml.apache.org/axis/}hostname:agave.wustl.edu
> 
> java.lang.reflect.InvocationTargetException
>         at 
> org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:221)
>         at 
> org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:128)
>         at 
> org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087)
>         at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown 
> Source)
>         at 
> org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown 
> Source)
>         at 
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown 
> Source)
>         at 
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown 
> Source)
>         at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>         at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>         at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>         at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
>         at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
>         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 
> edu.sdsc.nbcr.opal.GenericServiceClient.main(GenericServiceClient.java:311)
> 
> 
> At least it appears to be talking to Tomcat.  Here are the Tomcat logs:
> 
> 2009-06-24 13:39:55,205 INFO  
> edu.sdsc.nbcr.opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java:72) - 
> called
> 2009-06-24 13:39:55,308 INFO  
> edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) - Using 
> job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
> 2009-06-24 13:49:21,483 INFO  
> edu.sdsc.nbcr.opal.AppServiceImpl.launchJob(AppServiceImpl.java:237) - called
> 2009-06-24 13:49:21,485 INFO  
> edu.sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java:1038) - 
> called
> 2009-06-24 13:49:21,487 INFO  
> edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java:944) - 
> called
> 2009-06-24 13:49:21,500 INFO  
> edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's DN: Unknown 
> client
> 2009-06-24 13:49:21,502 INFO  
> edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's IP: 
> 127.0.0.1
> 2009-06-24 13:49:21,504 INFO  
> edu.sdsc.nbcr.opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java:72) - 
> called
> 2009-06-24 13:49:21,509 INFO  
> edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) - Using 
> job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
> 
> 
> I think I'm getting close ;-)
> 
> Thanks again for your help.
> 
> Malcolm
> 

Re: [Opaltoolkit-users] problem launching opal jobs

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

Luca,

On Wednesday 24 June 2009 01:02:42 pm Luca Clementi wrote:
> > After fixing it, I'm getting a different error when I try to submit a
> > job:
> >
> > [root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l
> > http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber
> > sample.pdb output.pqr" -f samples/sample.pdb
> > Exception in thread "main" java.lang.NoClassDefFoundError:
> > edu/sdsc/nbcr/opal/GenericServiceClient
> > Caused by: java.lang.ClassNotFoundException:
> > edu.sdsc.nbcr.opal.GenericServiceClient
> >         at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
> >         at java.security.AccessController.doPrivileged(Native Method)
> >         at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> >         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
> >         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
> > Could not find the main class: edu.sdsc.nbcr.opal.GenericServiceClient.  
> > Program will exit.
>
> Tobias,
> you have to set the classpath properly before you can use the Opal
> client. Please run
> . etc/classpath.sh
> if you are using bash.

I thought running the shell script would set the CLASSPATH, but for some weird 
reason it doesn't.  It just prints out the list of directories:

[root@agave opal-ws-2.0]# ./etc/classpath.sh 

[root@agave opal-ws-2.0]# echo $CLASSPATH

[root@agave opal-ws-2.0]# printenv | grep CLASS
[root@agave opal-ws-2.0]# 

It probably doesn't matter why it's failing.  I manually set it.
Here's what I see now:

[root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://agave:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
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:agave.wustl.edu

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 org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown 
Source)
        at 
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown 
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
        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 
edu.sdsc.nbcr.opal.GenericServiceClient.main(GenericServiceClient.java:311)


At least it appears to be talking to Tomcat.  Here are the Tomcat logs:

2009-06-24 13:39:55,205 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java:72) - 
called
2009-06-24 13:39:55,308 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) - Using 
job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager
2009-06-24 13:49:21,483 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchJob(AppServiceImpl.java:237) - called
2009-06-24 13:49:21,485 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.retrieveAppConfig(AppServiceImpl.java:1038) - 
called
2009-06-24 13:49:21,487 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.writeAppInput(AppServiceImpl.java:944) - 
called
2009-06-24 13:49:21,500 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteDN(Util.java:62) - Client's DN: Unknown 
client
2009-06-24 13:49:21,502 INFO  
edu.sdsc.nbcr.opal.util.Util.getRemoteIP(Util.java:43) - Client's IP: 
127.0.0.1
2009-06-24 13:49:21,504 INFO  
edu.sdsc.nbcr.opal.state.HibernateUtil.saveJobInfoInDatabase(HibernateUtil.java:72) - 
called
2009-06-24 13:49:21,509 INFO  
edu.sdsc.nbcr.opal.AppServiceImpl.launchApp(AppServiceImpl.java:579) - Using 
job manager class: edu.sdsc.nbcr.opal.manager.DRMAAJobManager


I think I'm getting close ;-)

Thanks again for your help.

Malcolm

-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Malcolm Tobias wrote:
> Luca,
> 
> On Tuesday 23 June 2009 04:46:55 pm Luca Clementi wrote:
>>>         {http://nbcr.sdsc.edu/opal/types}opalFaultOutput:<message>Can't
>>> instantiate Opal Job Manager - Job manager class
>>> edu.sdsc.ncbr.opal.manager.DRMAAJobManager not found</message>
>> Tobias,
>> you have to typo, it's nbcr not ncbr.
> 
> Doh!  Sorry I didn't catch that.
> 
> After fixing it, I'm getting a different error when I try to submit a job:
> 
> [root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
> http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
> sample.pdb output.pqr" -f samples/sample.pdb
> Exception in thread "main" java.lang.NoClassDefFoundError: 
> edu/sdsc/nbcr/opal/GenericServiceClient
> Caused by: java.lang.ClassNotFoundException: 
> edu.sdsc.nbcr.opal.GenericServiceClient
>         at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
>         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
> Could not find the main class: edu.sdsc.nbcr.opal.GenericServiceClient.  
> Program will exit.
> 

Tobias,
you have to set the classpath properly before you can use the Opal 
client. Please run
. etc/classpath.sh
if you are using bash.


>>> Is there some way to customize how Opal talking to the queuing system via
>>> DRMAA?
>> Not really. Unfortunately we use DRMAA so that we don't have to generate
>>   submission scripts for each scheduler (DRMAA is an API library).
>>
>> On our machine we don't use PBS but SGE and to specify a default queue
>> on our cluster we have used a SGE configuration file that can be placed
>> in the home of the user called .sge_request.
> 
> I couldn't find a similar configuration file for PBS/Torque so I was thinking
> about creating an alias for qsub.  This works for interactive logins, but I'm 
> not sure if it will work with DRMAA.  Any reasons why this wouldn't work?  

DRMAA uses APIs to talk with the scheduler, it doesn't use any command 
line. My guess is that it shouldn't work.

> Is there some log file that I should be check in case this doesn't work?
> 

All the log of Opal are in $CATALINA_HOME/logs/catalina.out

Tobias I would keep on looking in PBS documentation how to default a 
user to a particular queue.

Sincerely,
Luca

Re: [Opaltoolkit-users] problem launching opal jobs

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

Luca,

On Tuesday 23 June 2009 04:46:55 pm Luca Clementi wrote:
> >         {http://nbcr.sdsc.edu/opal/types}opalFaultOutput:<message>Can't
> > instantiate Opal Job Manager - Job manager class
> > edu.sdsc.ncbr.opal.manager.DRMAAJobManager not found</message>
>
> Tobias,
> you have to typo, it's nbcr not ncbr.

Doh!  Sorry I didn't catch that.

After fixing it, I'm getting a different error when I try to submit a job:

[root@agave opal-ws-2.0]# java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
sample.pdb output.pqr" -f samples/sample.pdb
Exception in thread "main" java.lang.NoClassDefFoundError: 
edu/sdsc/nbcr/opal/GenericServiceClient
Caused by: java.lang.ClassNotFoundException: 
edu.sdsc.nbcr.opal.GenericServiceClient
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
Could not find the main class: edu.sdsc.nbcr.opal.GenericServiceClient.  
Program will exit.

> > Is there some way to customize how Opal talking to the queuing system via
> > DRMAA?
>
> Not really. Unfortunately we use DRMAA so that we don't have to generate
>   submission scripts for each scheduler (DRMAA is an API library).
>
> On our machine we don't use PBS but SGE and to specify a default queue
> on our cluster we have used a SGE configuration file that can be placed
> in the home of the user called .sge_request.

I couldn't find a similar configuration file for PBS/Torque so I was thinking
about creating an alias for qsub.  This works for interactive logins, but I'm 
not sure if it will work with DRMAA.  Any reasons why this wouldn't work?  
Is there some log file that I should be check in case this doesn't work?

Cheers,
Malcolm


-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] problem launching opal jobs

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

Malcolm Tobias wrote:
> I'm attempting to set up our own local pdb2pqr Opal server following the
> instructions at:
> 
> http://www.nbcr.net/software/opal/docs/2.0/installation.html
> 
> After customizing the XML configuration to point to our local pdb2pqr, I 
> deployed the service:
> 
> ant deploy -DserviceName=pdb2pqr -DappConfig=./pdb2pqr_config.xml 
> 
> I then tried to use the client to launch a job:
> 
> java edu.sdsc.nbcr.opal.GenericServiceClient -l 
> http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
> sample.pdb output.pqr" -f samples/sample.pdb
> 
> Reading command line arguments
> Service URL: http://agave:8080/opal2/services/pdb2pqr
> Invoking operation: launchJob
> 
> Command line arguments: --ff=amber sample.pdb output.pqr
> Making non-blocking invocation on Opal service -
> Exception in thread "main" AxisFault
>  faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException
>  faultSubcode: 
>  faultString: 
>  faultActor: 
>  faultNode: 
>  faultDetail: 
>         {http://nbcr.sdsc.edu/opal/types}opalFaultOutput:<message>Can't 
> instantiate Opal Job Manager - Job manager class 
> edu.sdsc.ncbr.opal.manager.DRMAAJobManager not found</message>

Tobias,
you have to typo, it's nbcr not ncbr.

>         
> {http://xml.apache.org/axis/}exceptionName:edu.sdsc.nbcr.opal.FaultType
>         {http://xml.apache.org/axis/}hostname:agave.wustl.edu
> 
> The job manager that I have specified in my pdb2pqr_config.xml file is:
> 
> <jobManagerFQCN>edu.sdsc.ncbr.opal.manager.DRMAAJobManager</jobManagerFQCN>
> 
> The corresponding job manager defined in my etc/opal.properties is:
> 
>    opal.jobmanager=edu.sdsc.ncbr.opal.manager.DRMAAJobManager
> 
> Any ideas on what might be wrong?
> 
> 
> A second question that I'll need to address at some point is how to customize 
> the batch script that is used for launching the jobs.  We have an existing 
> cluster (running PBS/torque) and I'd like to define a property that denotes 
> that some special nodes are available for running Opal jobs.  If I were doing 
> this manually, instead of specifying:
> 
> qsub -I -lnodes=1
> 
> I'd do this by specifying:
> 
> qsub -I -lnodes=1:opal
> 
> Is there some way to customize how Opal talking to the queuing system via 
> DRMAA?
> 

Not really. Unfortunately we use DRMAA so that we don't have to generate 
  submission scripts for each scheduler (DRMAA is an API library).

On our machine we don't use PBS but SGE and to specify a default queue 
on our cluster we have used a SGE configuration file that can be placed 
in the home of the user called .sge_request.
Below an example we use to specify that opaluser (the user running 
opal-tomcat) should use the urgent queue by default. I'm sure that PBS 
has something similar.

Please let us know if you have any problem with torque/opal, since we 
never tested that configuration.

Sincerely,
Luca


[opaluser@kryptonite ~]$ tail .sge_request

-l urgent

[Opaltoolkit-users] problem launching opal jobs

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

I'm attempting to set up our own local pdb2pqr Opal server following the
instructions at:

http://www.nbcr.net/software/opal/docs/2.0/installation.html

After customizing the XML configuration to point to our local pdb2pqr, I 
deployed the service:

ant deploy -DserviceName=pdb2pqr -DappConfig=./pdb2pqr_config.xml 

I then tried to use the client to launch a job:

java edu.sdsc.nbcr.opal.GenericServiceClient -l 
http://agave:8080/opal2/services/pdb2pqr -r launchJob -a "--ff=amber 
sample.pdb output.pqr" -f samples/sample.pdb

Reading command line arguments
Service URL: http://agave:8080/opal2/services/pdb2pqr
Invoking operation: launchJob

Command line arguments: --ff=amber sample.pdb output.pqr
Making non-blocking invocation on Opal service -
Exception in thread "main" AxisFault
 faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException
 faultSubcode: 
 faultString: 
 faultActor: 
 faultNode: 
 faultDetail: 
        {http://nbcr.sdsc.edu/opal/types}opalFaultOutput:<message>Can't 
instantiate Opal Job Manager - Job manager class 
edu.sdsc.ncbr.opal.manager.DRMAAJobManager not found</message>
        
{http://xml.apache.org/axis/}exceptionName:edu.sdsc.nbcr.opal.FaultType
        {http://xml.apache.org/axis/}hostname:agave.wustl.edu

The job manager that I have specified in my pdb2pqr_config.xml file is:

<jobManagerFQCN>edu.sdsc.ncbr.opal.manager.DRMAAJobManager</jobManagerFQCN>

The corresponding job manager defined in my etc/opal.properties is:

   opal.jobmanager=edu.sdsc.ncbr.opal.manager.DRMAAJobManager

Any ideas on what might be wrong?


A second question that I'll need to address at some point is how to customize 
the batch script that is used for launching the jobs.  We have an existing 
cluster (running PBS/torque) and I'd like to define a property that denotes 
that some special nodes are available for running Opal jobs.  If I were doing 
this manually, instead of specifying:

qsub -I -lnodes=1

I'd do this by specifying:

qsub -I -lnodes=1:opal

Is there some way to customize how Opal talking to the queuing system via 
DRMAA?

Thanks,
Malcolm


-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] server configuration/build questions

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

Luca,

Thanks for your help clarifying the configuration settings.

I tried building again (after doing an 'ant clean' as suggested) and the
2nd time the build went through fine.  Maybe the 'ant clean' was necessary?

Thanks againm
Malcolm


On Monday 22 June 2009 01:05:21 pm Luca Clementi wrote:
> Malcolm Tobias wrote:
> > I'm attempting to set up my own local Opal server.
> >
> > I have a couple of configuration questions:
> >
> > - in etc/opal.properties, the examples for the opal.jobmanager parameter
> > read:
> >
> >     # full qualified class name (FQCN) of the job manager being used
> >     opal.jobmanager=edu.sdsc.nbcr.opal.manager.ForkJobManager
> >     # opal.jobmanager=edu.sdsc.nbcr.opal.manager.DRMAAJobManager
> >     # opal.jobmanager=edu.sdsc.nbcr.opal.manager.GlobusJobManager
> >     # opal.jobmanager=edu.sdsc.nbcr.opal.manager.RemoteGlobusJobManager
> >
> >    If my system is named foo.bar.com and I wanted to use DRMAA, would
> >    I use:
> >    opal.jobmanager=com.bar.foo.opal.manager.DRMAAJobManager ?
> >
> >    It's not clear whether the server used in the example is:
> >    opal.nbcr.sdsc.edu or nbcr.sdsc.edu or even manager.opal.nbcr.sdsc.edu
>
> Malcolm,
> You have to use the Java Class FQCN not your server domain name.
>
> So basically you don't have to change anything, simply uncomment the
> line you want to use and make sure to have only one line uncommented.
>
> E.g. for DRMAA:
>
> # full qualified class name (FQCN) of the job manager being used
> # opal.jobmanager=edu.sdsc.nbcr.opal.manager.ForkJobManager
> opal.jobmanager=edu.sdsc.nbcr.opal.manager.DRMAAJobManager
> # opal.jobmanager=edu.sdsc.nbcr.opal.manager.GlobusJobManager
> # opal.jobmanager=edu.sdsc.nbcr.opal.manager.RemoteGlobusJobManager
>
> > - step 3 reads:
> >
> > If you did not follow instructions to set up a real production database,
> > modify the connection.url property inside etc/hibernate-opal.cfg.xml from
> > jdbc:hsqldb:file:data/opaldb to
> > jdbc:hsqldb:file:<absolute_path_for_data_dir>/opaldb.
> >
> > 	I did not set up a real production database.  What path would I use
> > 	to the opaldb?  I don't see anything under the opal-ws-2.0/ directory.
>
> Just use the path where you would like to store your database data
> files. We generally use $CATALINA_HOME/data. Make sure your tomcat user
> can write in that directory and that it doesn't get deleted.
>
> > I also had one installation question.  During the initial install, the
> > 'ant install' step just hangs:
> >
> > [root@agave opal-ws-2.0]# ant install
> > Buildfile: build.xml
> >
> > setenv:
> >     [mkdir] Created dir: /usr/local/src/opal-ws-2.0/build
> >     [mkdir] Created dir: /usr/local/src/opal-ws-2.0/build/classes
> >
> > compile:
> > Trying to override old definition of task wsdl2java
> >
> > setenv:
> >
> > generateStubs:
> >     [mkdir] Created dir: /usr/local/src/opal-ws-2.0/build/gen
> > [wsdl2java] WSDL2Java /usr/local/src/opal-ws-2.0/wsdl/opal.wsdl
> >
> > This is an older system, but the tools need for installing are relatively
> > recent:
> >
> > [root@agave ~]# cat /etc/redhat-release
> > Fedora Core release 6 (Zod)
> >
> > [root@agave ~]# ant -version
> > Apache Ant version 1.7.1 compiled on June 27 2008
> > [root@agave ~]# java -version
> > java version "1.6.0_14"
> > Java(TM) SE Runtime Environment (build 1.6.0_14-b08)
> > Java HotSpot(TM) Client VM (build 14.0-b16, mixed mode, sharing)
> >
> > Any suggestions for debugging this installation problem?
>
> That's very odd. The wsdl2java might takes some time expecially on older
> system.
> Please give it another try, do a ant clean and then do another ant
> install, and try wait a little longer.
>
> If the process still hangs please let me know what the ant process is
> doing (is it just blocked, is it doing CPU, did it fork another process,
> etc.) the output of
> ps aux
> and
> ls build/gen/edu/sdsc/nbcr/opal/
> would be useful to further debug the problem.
>
> Sincerely,
> Luca



-- 
Malcolm Tobias
314.362.1594

Re: [Opaltoolkit-users] server configuration/build questions

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

Malcolm Tobias wrote:
> I'm attempting to set up my own local Opal server.
> 
> I have a couple of configuration questions:
> 
> - in etc/opal.properties, the examples for the opal.jobmanager parameter read:
> 
>     # full qualified class name (FQCN) of the job manager being used
>     opal.jobmanager=edu.sdsc.nbcr.opal.manager.ForkJobManager
>     # opal.jobmanager=edu.sdsc.nbcr.opal.manager.DRMAAJobManager
>     # opal.jobmanager=edu.sdsc.nbcr.opal.manager.GlobusJobManager
>     # opal.jobmanager=edu.sdsc.nbcr.opal.manager.RemoteGlobusJobManager
> 
>    If my system is named foo.bar.com and I wanted to use DRMAA, would
>    I use:
>    opal.jobmanager=com.bar.foo.opal.manager.DRMAAJobManager ?
> 
>    It's not clear whether the server used in the example is:
>    opal.nbcr.sdsc.edu or nbcr.sdsc.edu or even manager.opal.nbcr.sdsc.edu

Malcolm,
You have to use the Java Class FQCN not your server domain name.

So basically you don't have to change anything, simply uncomment the 
line you want to use and make sure to have only one line uncommented.

E.g. for DRMAA:

# full qualified class name (FQCN) of the job manager being used
# opal.jobmanager=edu.sdsc.nbcr.opal.manager.ForkJobManager
opal.jobmanager=edu.sdsc.nbcr.opal.manager.DRMAAJobManager
# opal.jobmanager=edu.sdsc.nbcr.opal.manager.GlobusJobManager
# opal.jobmanager=edu.sdsc.nbcr.opal.manager.RemoteGlobusJobManager

> - step 3 reads:
> 
> If you did not follow instructions to set up a real production database, 
> modify the connection.url property inside etc/hibernate-opal.cfg.xml from 
> jdbc:hsqldb:file:data/opaldb to 
> jdbc:hsqldb:file:<absolute_path_for_data_dir>/opaldb.
> 
> 	I did not set up a real production database.  What path would I use
> 	to the opaldb?  I don't see anything under the opal-ws-2.0/ directory.

Just use the path where you would like to store your database data 
files. We generally use $CATALINA_HOME/data. Make sure your tomcat user 
can write in that directory and that it doesn't get deleted.

> I also had one installation question.  During the initial install, the 'ant 
> install' step just hangs:
> 
> [root@agave opal-ws-2.0]# ant install
> Buildfile: build.xml
> 
> setenv:
>     [mkdir] Created dir: /usr/local/src/opal-ws-2.0/build
>     [mkdir] Created dir: /usr/local/src/opal-ws-2.0/build/classes
> 
> compile:
> Trying to override old definition of task wsdl2java
> 
> setenv:
> 
> generateStubs:
>     [mkdir] Created dir: /usr/local/src/opal-ws-2.0/build/gen
> [wsdl2java] WSDL2Java /usr/local/src/opal-ws-2.0/wsdl/opal.wsdl
> 
> This is an older system, but the tools need for installing are relatively 
> recent:
> 
> [root@agave ~]# cat /etc/redhat-release 
> Fedora Core release 6 (Zod)
> 
> [root@agave ~]# ant -version
> Apache Ant version 1.7.1 compiled on June 27 2008
> [root@agave ~]# java -version
> java version "1.6.0_14"
> Java(TM) SE Runtime Environment (build 1.6.0_14-b08)
> Java HotSpot(TM) Client VM (build 14.0-b16, mixed mode, sharing)
> 
> Any suggestions for debugging this installation problem?


That's very odd. The wsdl2java might takes some time expecially on older 
system.
Please give it another try, do a ant clean and then do another ant 
install, and try wait a little longer.

If the process still hangs please let me know what the ant process is 
doing (is it just blocked, is it doing CPU, did it fork another process, 
etc.) the output of
ps aux
and
ls build/gen/edu/sdsc/nbcr/opal/
would be useful to further debug the problem.

Sincerely,
Luca

[Opaltoolkit-users] server configuration/build questions

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

I'm attempting to set up my own local Opal server.

I have a couple of configuration questions:

- in etc/opal.properties, the examples for the opal.jobmanager parameter read:

    # full qualified class name (FQCN) of the job manager being used
    opal.jobmanager=edu.sdsc.nbcr.opal.manager.ForkJobManager
    # opal.jobmanager=edu.sdsc.nbcr.opal.manager.DRMAAJobManager
    # opal.jobmanager=edu.sdsc.nbcr.opal.manager.GlobusJobManager
    # opal.jobmanager=edu.sdsc.nbcr.opal.manager.RemoteGlobusJobManager

   If my system is named foo.bar.com and I wanted to use DRMAA, would
   I use:
   opal.jobmanager=com.bar.foo.opal.manager.DRMAAJobManager ?

   It's not clear whether the server used in the example is:
   opal.nbcr.sdsc.edu or nbcr.sdsc.edu or even manager.opal.nbcr.sdsc.edu

- step 3 reads:

If you did not follow instructions to set up a real production database, 
modify the connection.url property inside etc/hibernate-opal.cfg.xml from 
jdbc:hsqldb:file:data/opaldb to 
jdbc:hsqldb:file:<absolute_path_for_data_dir>/opaldb.

	I did not set up a real production database.  What path would I use
	to the opaldb?  I don't see anything under the opal-ws-2.0/ directory.

I also had one installation question.  During the initial install, the 'ant 
install' step just hangs:

[root@agave opal-ws-2.0]# ant install
Buildfile: build.xml

setenv:
    [mkdir] Created dir: /usr/local/src/opal-ws-2.0/build
    [mkdir] Created dir: /usr/local/src/opal-ws-2.0/build/classes

compile:
Trying to override old definition of task wsdl2java

setenv:

generateStubs:
    [mkdir] Created dir: /usr/local/src/opal-ws-2.0/build/gen
[wsdl2java] WSDL2Java /usr/local/src/opal-ws-2.0/wsdl/opal.wsdl

This is an older system, but the tools need for installing are relatively 
recent:

[root@agave ~]# cat /etc/redhat-release 
Fedora Core release 6 (Zod)

[root@agave ~]# ant -version
Apache Ant version 1.7.1 compiled on June 27 2008
[root@agave ~]# java -version
java version "1.6.0_14"
Java(TM) SE Runtime Environment (build 1.6.0_14-b08)
Java HotSpot(TM) Client VM (build 14.0-b16, mixed mode, sharing)

Any suggestions for debugging this installation problem?

Malcolm


-- 
Malcolm Tobias
314.362.1594