opaltoolkit-users — Users mailing-list for Opal Toolkit

Re: [Opaltoolkit-users] Deploying Emboss in Opal2

[Jane R. <j2...@uc...>]

Hi Jeroen,

First of all, can you run emboss from the command line directly?

Also, did you see "the quested resource () is not available" after you clicked on "submit" from the opal web form?

Jane


________________________________________
From: jeroen vannevel [jer...@ho...]
Sent: Friday, July 08, 2011 5:02 AM
To: opa...@li...
Subject: [Opaltoolkit-users] Deploying Emboss in Opal2

Hello

I've installed Opal2 on my Tomcat 5.5.33 server and now I'd like to make the emboss programs available in this.
I've been working on this for two days and I just seem to trample at the same spot.
Perhaps someone has the required files or could tell me how to deal with this specific case?
I've tried compiling all the emboss programs and put them in a .war package but after uploading this to Tomcat I just keep getting
'The requested resource () is not available.' error messages.

Yours
Jeroen V.

[Opaltoolkit-users] Deploying Emboss in Opal2

[jeroen v. <jer...@ho...>]

Hello
 
I've installed Opal2 on my Tomcat 5.5.33 server and now I'd like to make the emboss programs available in this.
I've been working on this for two days and I just seem to trample at the same spot.
Perhaps someone has the required files or could tell me how to deal with this specific case?
I've tried compiling all the emboss programs and put them in a .war package but after uploading this to Tomcat I just keep getting 
'The requested resource () is not available.' error messages.
 
Yours
Jeroen V. 		 	   		  

[Opaltoolkit-users] Opal Toolkit Rocks Roll 5.4 Released

[nadya w. <na...@sd...>]

+----------------------------------------------------------------------- 
--+

                      Opal Roll 5.4 Release Announcement

+----------------------------------------------------------------------- 
--+

The National Biomedical Computation Resource  at University of  
California,
San Diego is pleased to announce the availability of Opal Roll  
package for
Rocks clusters version 5.4

The Opal Toolkit provides a mechanism rapid wrapping existing scientific
applications as Web services and exposing the services to various  
clients.
It includes job and data management and state management (by storing the
service state via Hibernate into MySQL). The applications are  
deployed as
services and are available to end users via a remote access.

The Opal Roll simplifies Opal Toolkit deployment and integration on   
Rocks
clusters (http://www.rocksclusters.org). More information about Opal  
Toolkit
can be found at http://apbs.sourceforge.net/ or at http://opal.nbcr.net.

This Opal Roll contains the latest Opal Toolkit version 2.4, apache  
tomcat
version 5.5.17 and tomcat-connectors version 1.2.31.  It requires SGE  
roll
to be installed.

The Opal Roll can be downloaded from NBCR download site
http://www.nbcr.net/software/downloads/rolls and the Roll documentation
including installation and usage information is available at
http://nbcr.net/software/doc/opal-roll/5.4

Questions or comments about the roll may be directed to NBCR support
su...@nb...


Nadya Williams                 University of California, San Diego
na...@sd...             9500 Gilman Dr. MC 0446
+1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
+1 858 822 1619 (fax)      USA

[Opaltoolkit-users] Opal Workflow Plugins for Taverna, Vision, and VisTrails Released

[Jane R. <j2...@uc...>]

Dear users,

We are pleased to announce the releases of Opal plugins for VisTrails, Taverna, and Kepler.
Our Opal plugins allows the user to use any Opal 2.x services from VisTrails, Taverna, and Kepler,
and construct workflows based on Opal services.  Each of each workflow tools automatically
generates a GUI for each Opal web service.

Documentation for these Opal plugins can be found at

VisTrails (tested w version 1.5): https://www.nbcr.net/pub/wiki/index.php?title=VisTrails
Taverna (tested w version 2.2):   https://www.nbcr.net/pub/wiki/index.php?title=Taverna
Kepler (tested w version 2):      https://www.nbcr.net/pub/wiki/index.php?title=Kepler

Sincerely,
NBCR

[Opaltoolkit-users] Opal 2.4 Release

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

We are pleased to announce the release of version 2.4 of the Opal  
Toolkit.

New features in the 2.4 release of Opal include:
- Additional operation added to Opal WSDL and AppService  
implementation to get system information (number of jobs running/ 
queued, job manager type, data lifetime, etc)
- Updated database schema to support ACTIVE/INACTIVE service status,  
which will be used while plotting usage information. Inactive services  
will not be plotted. This feature is not available for HSQL DB
- Ability to set the DRMAA queue in the opal.properties, and override  
it in the application configuration
- A set of absolute paths now accessible to applications via the  
opal.properties. In the past applications only had access to the Opal  
working directory
- Support for recursive listing of output directories for the  
getOutputs() operation

Bug fixes include:
- Reset of error messages on the Dashboard, which were never reset in  
the prior release
- Usage Statistics fixes
-- Checking/unchecking boxes, which didn't work in the prior release
-- Error in the calculation of jobs when the services had similar names

Opal 2.4 can be downloaded from here: https://sourceforge.net/projects/opaltoolkit/files/ 
.

Sincerely,
Opal Team

Re: [Opaltoolkit-users] Installation problems

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

Hi Dan,

It is indeed documented on the prerequisites - http://www.nbcr.net/software/opal/docs/2.X/serverprerequisites.html 
. Maybe we should make it more prominent.

It is indeed a configuration difference - the directory structures are  
somewhat different in 6.0 and higher. So we will probably have to  
update our install scripts.

Thanks for the feedback!
Sriram

On Oct 4, 2010, at 11:23 AM, Daniel Blezek wrote:

> Sriram,
>
>  Tomcat 5.5 worked.  This should be documented on the website.  I  
> choose 7
> first, then 6 and finally 5.  I would suggest supporting more recent
> versions of Tomcat.  I suspect it is simply a configuration difference
> between the versions...
>
> Thanks for the help,
> -dan
>
>
> On 10/4/10 12:54 PM, "Sriram Krishnan" <sr...@sd...> wrote:
>
>> Hi Daniel,
>>
>> Please do cc the mailing list - I hope this is useful to others as  
>> well.
>>
>> One thing that jumps from your logs is that you are using Tomcat
>> 6.0.29. Opal2 has only been verified to work with Tomcat 5.X. Would
>> you mind testing it out with either 5.0.30 or 5.5? I would be
>> surprised if that doesn't work, because we have not seen this error
>> before for those versions.
>>
>> If there is sufficient interest in using 6.0, we could plan on
>> supporting it in the future.
>>
>> Thanks,
>> Sriram
>>
>> On Oct 4, 2010, at 10:49 AM, Daniel Blezek wrote:
>>
>>> Sriram,
>>>
>>> (Keeping on the list in the hopes that others will benefit.)
>>>
>>> Here is the listing of Tomcat’s directory:
>>>
>>> [mi3c@mi3c-jobs apache-tomcat-6.0.29]$ ls webapps/opal2/WEB-INF/lib
>>> activation-1_0_2.jar         javamail-1.4.3.jar
>>> ant-1.7.0.jar                javassist-3.4.GA.jar
>>> antlr-2.7.6.jar              jaxrpc.jar
>>> axis-ant.jar                 jcommon-1.0.12.jar
>>> axis.jar                     jdom-1.1.jar
>>> c3p0-0.9.1.2.jar             jfreechart-1.0.8.jar
>>> cglib-2.1.3.jar              jstl.jar
>>> classad.jar                  jta-1.1.jar
>>> commons-beanutils-1.7.0.jar  mailapi-1_3_1.jar
>>> commons-chain-1.1.jar        mysql-connector-java-5.1.8-bin.jar
>>> commons-cli-2.0.jar          opal-ws-2.3.1.jar
>>> commons-collections-3.1.jar  oro-2.0.8.jar
>>> commons-digester-1.8.jar     postgresql-8.2-506.jdbc3.jar
>>> commons-discovery-0.2.jar    rome-1.0RC1.jar
>>> commons-fileupload-1.2.jar   saaj.jar
>>> commons-io-1.4.jar           slf4j-api-1.5.2.jar
>>> commons-logging-1.0.4.jar    slf4j-log4j12-1.5.2.jar
>>> commons-validator-1.3.1.jar  standard.jar
>>> db2jcc.jar                   struts-core-1.3.8.jar
>>> dom4j-1.6.1.jar              struts-extras-1.3.8.jar
>>> drmaa.jar                    struts-taglib-1.3.8.jar
>>> hibernate3.jar               wsdl4j-1.5.1.jar
>>> hsqldb.jar
>>>
>>>
>>> It looks like everything is installed (opal-ws-2.3.1.jar).  I did
>>> restart
>>> Tomcat a few times.  No errors on install.
>>>
>>> Please let me know what I can send to you to help debug this...
>>>
>>> Thanks,
>>> -dan
>>>
>>>
>>> On 10/4/10 12:01 PM, "Sriram Krishnan" <sr...@sd...> wrote:
>>>
>>>> Hi Daniel,
>>>>
>>>> It appears as if none of the Opal jars can be found. Did you
>>>> restart Tomcat
>>>> after Opal installation? At this point, Opal can't be hot-deployed,
>>>> and you
>>>> will have to restart your Tomcat after installation. If you have
>>>> indeed
>>>> restarted, please check your CATALINA_HOME/webapps/opal2/WEB-INF/
>>>> lib to see if
>>>> all the Opal jars are present. If they aren't, something went wrong
>>>> with the
>>>> installation.
>>>>
>>>> A list of Opal services is provided by Axis, e.g.
>>>> http://ws.nbcr.net/opal2/services. Does that not work for you?
>>>>
>>>> Cheers,
>>>> Sriram
>>>>
>>>> On Oct 4, 2010, at 9:16 AM, Daniel Blezek wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>>  We’re using Taverna ( http://www.taverna.org.uk/) as our
>>>>> workflow engine,
>>>>> and would like to expose some of our command line apps.  I was
>>>>> able to
>>>>> connect to the getVersion service.  When I tried to install the
>>>>> date service,
>>>>> I get this error (in the tomcat log):
>>>>>
>>>>> Oct 4, 2010 11:10:06 AM
>>>>> org.apache.catalina.core.StandardWrapperValve invoke
>>>>> SEVERE: Servlet.service() for servlet [AxisServlet] in context
>>>>> with path
>>>>> [/opal2] threw exce
>>>>> ption [Servlet execution threw an exception] with root cause
>>>>> java.lang.NoClassDefFoundError: Could not initialize class
>>>>> edu.sdsc.nbcr.opal.AppServiceImpl
>>>>>    at java.lang.Class.forName0(Native Method)
>>>>>    at java.lang.Class.forName(Class.java:247)
>>>>> <snip>
>>>>>
>>>>> And the List page doesn’t show any services.
>>>>>
>>>>> I also can’t connect to the dashboard:
>>>>>
>>>>> java.lang.NoClassDefFoundError: Could not initialize class
>>>>> edu.sdsc.nbcr.opal.state.HibernateUtil
>>>>>
>>>>> edu
>>>>> .sdsc
>>>>> .nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java: 
>>>>> 73)
>>>>>
>>>>> edu
>>>>> .sdsc
>>>>> .nbcr
>>>>> .opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.jav
>>>>> a:109)
>>>>>
>>>>> org
>>>>> .apache
>>>>> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java: 
>>>>> 108)
>>>>>
>>>>>
>>>>> Any help?
>>>>>
>>>>> Also: is there some way to publish all the services on one URL so
>>>>> Taverna
>>>>> will grab all of them rather than one at a time?
>>>>>
>>>>> Thanks,
>>>>> -dan
>>>>>
>>>>> -- 
>>>>> Daniel Blezek, PhD
>>>>> Medical Imaging Informatics Innovation Center
>>>>>
>>>>> P 127 or (77) 8 8886
>>>>> T 507 538 8886
>>>>> E ble...@ma...
>>>>>
>>>>> Mayo Clinic
>>>>> 200 First St. S.W.
>>>>> Harwick SL-44
>>>>> Rochester, MN 55905
>>>>> mayoclinic.org
>>>>> "It is more complicated than you think." -- RFC 1925
>>>>>
>>>>>
>>>>>
>>> -----------------------------------------------------------------------------
>>>>
>>>>
>>> -
>>>>> Virtualization is moving to the mainstream and overtaking non-
>>>>> virtualized
>>>>> environment for deploying applications. Does it make network
>>>>> security
>>>>> easier or more difficult to achieve? Read this whitepaper to
>>>>> separate the
>>>>> two and get a better understanding.
>>>>> http://p.sf.net/sfu/hp-phase2-d2d__________________________________________
>>>>> __
>>>>> ___
>>>>> Opaltoolkit-users mailing list
>>>>> Opa...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>>>
>>>>
>>>
>>> -- 
>>> Daniel Blezek, PhD
>>> Medical Imaging Informatics Innovation Center
>>>
>>> P 127 or (77) 8 8886
>>> T 507 538 8886
>>> E ble...@ma...
>>>
>>> Mayo Clinic
>>> 200 First St. S.W.
>>> Harwick SL-44
>>> Rochester, MN 55905
>>> mayoclinic.org
>>> "It is more complicated than you think." -- RFC 1925
>>
>
> -- 
> Daniel Blezek, PhD
> Medical Imaging Informatics Innovation Center
>
> P 127 or (77) 8 8886
> T 507 538 8886
> E ble...@ma...
>
> Mayo Clinic
> 200 First St. S.W.
> Harwick SL-44
> Rochester, MN 55905
> mayoclinic.org
> "It is more complicated than you think." -- RFC 1925

Re: [Opaltoolkit-users] Installation problems

[Daniel B. <Ble...@ma...>]

Sriram,

  Tomcat 5.5 worked.  This should be documented on the website.  I choose 7
first, then 6 and finally 5.  I would suggest supporting more recent
versions of Tomcat.  I suspect it is simply a configuration difference
between the versions...

Thanks for the help,
-dan


On 10/4/10 12:54 PM, "Sriram Krishnan" <sr...@sd...> wrote:

> Hi Daniel,
> 
> Please do cc the mailing list - I hope this is useful to others as well.
> 
> One thing that jumps from your logs is that you are using Tomcat
> 6.0.29. Opal2 has only been verified to work with Tomcat 5.X. Would
> you mind testing it out with either 5.0.30 or 5.5? I would be
> surprised if that doesn't work, because we have not seen this error
> before for those versions.
> 
> If there is sufficient interest in using 6.0, we could plan on
> supporting it in the future.
> 
> Thanks,
> Sriram
> 
> On Oct 4, 2010, at 10:49 AM, Daniel Blezek wrote:
> 
>> Sriram,
>> 
>> (Keeping on the list in the hopes that others will benefit.)
>> 
>> Here is the listing of Tomcat¹s directory:
>> 
>> [mi3c@mi3c-jobs apache-tomcat-6.0.29]$ ls webapps/opal2/WEB-INF/lib
>> activation-1_0_2.jar         javamail-1.4.3.jar
>> ant-1.7.0.jar                javassist-3.4.GA.jar
>> antlr-2.7.6.jar              jaxrpc.jar
>> axis-ant.jar                 jcommon-1.0.12.jar
>> axis.jar                     jdom-1.1.jar
>> c3p0-0.9.1.2.jar             jfreechart-1.0.8.jar
>> cglib-2.1.3.jar              jstl.jar
>> classad.jar                  jta-1.1.jar
>> commons-beanutils-1.7.0.jar  mailapi-1_3_1.jar
>> commons-chain-1.1.jar        mysql-connector-java-5.1.8-bin.jar
>> commons-cli-2.0.jar          opal-ws-2.3.1.jar
>> commons-collections-3.1.jar  oro-2.0.8.jar
>> commons-digester-1.8.jar     postgresql-8.2-506.jdbc3.jar
>> commons-discovery-0.2.jar    rome-1.0RC1.jar
>> commons-fileupload-1.2.jar   saaj.jar
>> commons-io-1.4.jar           slf4j-api-1.5.2.jar
>> commons-logging-1.0.4.jar    slf4j-log4j12-1.5.2.jar
>> commons-validator-1.3.1.jar  standard.jar
>> db2jcc.jar                   struts-core-1.3.8.jar
>> dom4j-1.6.1.jar              struts-extras-1.3.8.jar
>> drmaa.jar                    struts-taglib-1.3.8.jar
>> hibernate3.jar               wsdl4j-1.5.1.jar
>> hsqldb.jar
>> 
>> 
>> It looks like everything is installed (opal-ws-2.3.1.jar).  I did
>> restart
>> Tomcat a few times.  No errors on install.
>> 
>> Please let me know what I can send to you to help debug this...
>> 
>> Thanks,
>> -dan
>> 
>> 
>> On 10/4/10 12:01 PM, "Sriram Krishnan" <sr...@sd...> wrote:
>> 
>>> Hi Daniel,
>>> 
>>> It appears as if none of the Opal jars can be found. Did you
>>> restart Tomcat
>>> after Opal installation? At this point, Opal can't be hot-deployed,
>>> and you
>>> will have to restart your Tomcat after installation. If you have
>>> indeed
>>> restarted, please check your CATALINA_HOME/webapps/opal2/WEB-INF/
>>> lib to see if
>>> all the Opal jars are present. If they aren't, something went wrong
>>> with the
>>> installation.
>>> 
>>> A list of Opal services is provided by Axis, e.g.
>>> http://ws.nbcr.net/opal2/services. Does that not work for you?
>>> 
>>> Cheers,
>>> Sriram
>>> 
>>> On Oct 4, 2010, at 9:16 AM, Daniel Blezek wrote:
>>> 
>>>> Hi,
>>>> 
>>>>   We¹re using Taverna ( http://www.taverna.org.uk/) as our
>>>> workflow engine,
>>>> and would like to expose some of our command line apps.  I was
>>>> able to
>>>> connect to the getVersion service.  When I tried to install the
>>>> date service,
>>>> I get this error (in the tomcat log):
>>>> 
>>>> Oct 4, 2010 11:10:06 AM
>>>> org.apache.catalina.core.StandardWrapperValve invoke
>>>> SEVERE: Servlet.service() for servlet [AxisServlet] in context
>>>> with path
>>>> [/opal2] threw exce
>>>> ption [Servlet execution threw an exception] with root cause
>>>> java.lang.NoClassDefFoundError: Could not initialize class
>>>> edu.sdsc.nbcr.opal.AppServiceImpl
>>>>     at java.lang.Class.forName0(Native Method)
>>>>     at java.lang.Class.forName(Class.java:247)
>>>> <snip>
>>>> 
>>>> And the List page doesn¹t show any services.
>>>> 
>>>> I also can¹t connect to the dashboard:
>>>> 
>>>> java.lang.NoClassDefFoundError: Could not initialize class
>>>> edu.sdsc.nbcr.opal.state.HibernateUtil
>>>> 
>>>> edu 
>>>> .sdsc 
>>>> .nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:73)
>>>> 
>>>> edu 
>>>> .sdsc 
>>>> .nbcr 
>>>> .opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.jav
>>>> a:109)
>>>> 
>>>> org 
>>>> .apache 
>>>> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:108)
>>>> 
>>>> 
>>>> Any help?
>>>> 
>>>> Also: is there some way to publish all the services on one URL so
>>>> Taverna
>>>> will grab all of them rather than one at a time?
>>>> 
>>>> Thanks,
>>>> -dan
>>>> 
>>>> -- 
>>>> Daniel Blezek, PhD
>>>> Medical Imaging Informatics Innovation Center
>>>> 
>>>> P 127 or (77) 8 8886
>>>> T 507 538 8886
>>>> E ble...@ma...
>>>> 
>>>> Mayo Clinic
>>>> 200 First St. S.W.
>>>> Harwick SL-44
>>>> Rochester, MN 55905
>>>> mayoclinic.org
>>>> "It is more complicated than you think." -- RFC 1925
>>>> 
>>>> 
>>>> 
>> -----------------------------------------------------------------------------
>> > 
>>> 
>> -
>>>> Virtualization is moving to the mainstream and overtaking non-
>>>> virtualized
>>>> environment for deploying applications. Does it make network
>>>> security
>>>> easier or more difficult to achieve? Read this whitepaper to
>>>> separate the
>>>> two and get a better understanding.
>>>> http://p.sf.net/sfu/hp-phase2-d2d__________________________________________
>>>> __
>>>> ___
>>>> Opaltoolkit-users mailing list
>>>> Opa...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>> 
>>> 
>> 
>> -- 
>> Daniel Blezek, PhD
>> Medical Imaging Informatics Innovation Center
>> 
>> P 127 or (77) 8 8886
>> T 507 538 8886
>> E ble...@ma...
>> 
>> Mayo Clinic
>> 200 First St. S.W.
>> Harwick SL-44
>> Rochester, MN 55905
>> mayoclinic.org
>> "It is more complicated than you think." -- RFC 1925
> 

-- 
Daniel Blezek, PhD
Medical Imaging Informatics Innovation Center

P 127 or (77) 8 8886
T 507 538 8886
E ble...@ma...

Mayo Clinic
200 First St. S.W.
Harwick SL-44
Rochester, MN 55905
mayoclinic.org
"It is more complicated than you think." -- RFC 1925

Re: [Opaltoolkit-users] Installation problems

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

Hi Daniel,

Please do cc the mailing list - I hope this is useful to others as well.

One thing that jumps from your logs is that you are using Tomcat  
6.0.29. Opal2 has only been verified to work with Tomcat 5.X. Would  
you mind testing it out with either 5.0.30 or 5.5? I would be  
surprised if that doesn't work, because we have not seen this error  
before for those versions.

If there is sufficient interest in using 6.0, we could plan on  
supporting it in the future.

Thanks,
Sriram

On Oct 4, 2010, at 10:49 AM, Daniel Blezek wrote:

> Sriram,
>
> (Keeping on the list in the hopes that others will benefit.)
>
> Here is the listing of Tomcat’s directory:
>
> [mi3c@mi3c-jobs apache-tomcat-6.0.29]$ ls webapps/opal2/WEB-INF/lib
> activation-1_0_2.jar         javamail-1.4.3.jar
> ant-1.7.0.jar                javassist-3.4.GA.jar
> antlr-2.7.6.jar              jaxrpc.jar
> axis-ant.jar                 jcommon-1.0.12.jar
> axis.jar                     jdom-1.1.jar
> c3p0-0.9.1.2.jar             jfreechart-1.0.8.jar
> cglib-2.1.3.jar              jstl.jar
> classad.jar                  jta-1.1.jar
> commons-beanutils-1.7.0.jar  mailapi-1_3_1.jar
> commons-chain-1.1.jar        mysql-connector-java-5.1.8-bin.jar
> commons-cli-2.0.jar          opal-ws-2.3.1.jar
> commons-collections-3.1.jar  oro-2.0.8.jar
> commons-digester-1.8.jar     postgresql-8.2-506.jdbc3.jar
> commons-discovery-0.2.jar    rome-1.0RC1.jar
> commons-fileupload-1.2.jar   saaj.jar
> commons-io-1.4.jar           slf4j-api-1.5.2.jar
> commons-logging-1.0.4.jar    slf4j-log4j12-1.5.2.jar
> commons-validator-1.3.1.jar  standard.jar
> db2jcc.jar                   struts-core-1.3.8.jar
> dom4j-1.6.1.jar              struts-extras-1.3.8.jar
> drmaa.jar                    struts-taglib-1.3.8.jar
> hibernate3.jar               wsdl4j-1.5.1.jar
> hsqldb.jar
>
>
> It looks like everything is installed (opal-ws-2.3.1.jar).  I did  
> restart
> Tomcat a few times.  No errors on install.
>
> Please let me know what I can send to you to help debug this...
>
> Thanks,
> -dan
>
>
> On 10/4/10 12:01 PM, "Sriram Krishnan" <sr...@sd...> wrote:
>
>> Hi Daniel,
>>
>> It appears as if none of the Opal jars can be found. Did you  
>> restart Tomcat
>> after Opal installation? At this point, Opal can't be hot-deployed,  
>> and you
>> will have to restart your Tomcat after installation. If you have  
>> indeed
>> restarted, please check your CATALINA_HOME/webapps/opal2/WEB-INF/ 
>> lib to see if
>> all the Opal jars are present. If they aren't, something went wrong  
>> with the
>> installation.
>>
>> A list of Opal services is provided by Axis, e.g.
>> http://ws.nbcr.net/opal2/services. Does that not work for you?
>>
>> Cheers,
>> Sriram
>>
>> On Oct 4, 2010, at 9:16 AM, Daniel Blezek wrote:
>>
>>> Hi,
>>>
>>>   We’re using Taverna ( http://www.taverna.org.uk/) as our  
>>> workflow engine,
>>> and would like to expose some of our command line apps.  I was  
>>> able to
>>> connect to the getVersion service.  When I tried to install the  
>>> date service,
>>> I get this error (in the tomcat log):
>>>
>>> Oct 4, 2010 11:10:06 AM  
>>> org.apache.catalina.core.StandardWrapperValve invoke
>>> SEVERE: Servlet.service() for servlet [AxisServlet] in context  
>>> with path
>>> [/opal2] threw exce
>>> ption [Servlet execution threw an exception] with root cause
>>> java.lang.NoClassDefFoundError: Could not initialize class
>>> edu.sdsc.nbcr.opal.AppServiceImpl
>>>     at java.lang.Class.forName0(Native Method)
>>>     at java.lang.Class.forName(Class.java:247)
>>> <snip>
>>>
>>> And the List page doesn’t show any services.
>>>
>>> I also can’t connect to the dashboard:
>>>
>>> java.lang.NoClassDefFoundError: Could not initialize class
>>> edu.sdsc.nbcr.opal.state.HibernateUtil
>>>
>>> edu 
>>> .sdsc 
>>> .nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:73)
>>>
>>> edu 
>>> .sdsc 
>>> .nbcr 
>>> .opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.jav
>>> a:109)
>>>
>>> org 
>>> .apache 
>>> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:108)
>>>
>>>
>>> Any help?
>>>
>>> Also: is there some way to publish all the services on one URL so  
>>> Taverna
>>> will grab all of them rather than one at a time?
>>>
>>> Thanks,
>>> -dan
>>>
>>> -- 
>>> Daniel Blezek, PhD
>>> Medical Imaging Informatics Innovation Center
>>>
>>> P 127 or (77) 8 8886
>>> T 507 538 8886
>>> E ble...@ma...
>>>
>>> Mayo Clinic
>>> 200 First St. S.W.
>>> Harwick SL-44
>>> Rochester, MN 55905
>>> mayoclinic.org
>>> "It is more complicated than you think." -- RFC 1925
>>>
>>>
>>>
> -----------------------------------------------------------------------------> 
> >
> -
>>> Virtualization is moving to the mainstream and overtaking non- 
>>> virtualized
>>> environment for deploying applications. Does it make network  
>>> security
>>> easier or more difficult to achieve? Read this whitepaper to  
>>> separate the
>>> two and get a better understanding.
>>> http://p.sf.net/sfu/hp-phase2-d2d____________________________________________
>>> ___
>>> Opaltoolkit-users mailing list
>>> Opa...@li...
>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>
>>
>
> -- 
> Daniel Blezek, PhD
> Medical Imaging Informatics Innovation Center
>
> P 127 or (77) 8 8886
> T 507 538 8886
> E ble...@ma...
>
> Mayo Clinic
> 200 First St. S.W.
> Harwick SL-44
> Rochester, MN 55905
> mayoclinic.org
> "It is more complicated than you think." -- RFC 1925

Re: [Opaltoolkit-users] Installation problems

[Daniel B. <Ble...@ma...>]

Sriram,

 (Keeping on the list in the hopes that others will benefit.)

Here is the listing of Tomcat¹s directory:

[mi3c@mi3c-jobs apache-tomcat-6.0.29]$ ls webapps/opal2/WEB-INF/lib
activation-1_0_2.jar         javamail-1.4.3.jar
ant-1.7.0.jar                javassist-3.4.GA.jar
antlr-2.7.6.jar              jaxrpc.jar
axis-ant.jar                 jcommon-1.0.12.jar
axis.jar                     jdom-1.1.jar
c3p0-0.9.1.2.jar             jfreechart-1.0.8.jar
cglib-2.1.3.jar              jstl.jar
classad.jar                  jta-1.1.jar
commons-beanutils-1.7.0.jar  mailapi-1_3_1.jar
commons-chain-1.1.jar        mysql-connector-java-5.1.8-bin.jar
commons-cli-2.0.jar          opal-ws-2.3.1.jar
commons-collections-3.1.jar  oro-2.0.8.jar
commons-digester-1.8.jar     postgresql-8.2-506.jdbc3.jar
commons-discovery-0.2.jar    rome-1.0RC1.jar
commons-fileupload-1.2.jar   saaj.jar
commons-io-1.4.jar           slf4j-api-1.5.2.jar
commons-logging-1.0.4.jar    slf4j-log4j12-1.5.2.jar
commons-validator-1.3.1.jar  standard.jar
db2jcc.jar                   struts-core-1.3.8.jar
dom4j-1.6.1.jar              struts-extras-1.3.8.jar
drmaa.jar                    struts-taglib-1.3.8.jar
hibernate3.jar               wsdl4j-1.5.1.jar
hsqldb.jar


It looks like everything is installed (opal-ws-2.3.1.jar).  I did restart
Tomcat a few times.  No errors on install.

Please let me know what I can send to you to help debug this...

Thanks,
-dan


On 10/4/10 12:01 PM, "Sriram Krishnan" <sr...@sd...> wrote:

> Hi Daniel,
> 
> It appears as if none of the Opal jars can be found. Did you restart Tomcat
> after Opal installation? At this point, Opal can't be hot-deployed, and you
> will have to restart your Tomcat after installation. If you have indeed
> restarted, please check your CATALINA_HOME/webapps/opal2/WEB-INF/lib to see if
> all the Opal jars are present. If they aren't, something went wrong with the
> installation.
> 
> A list of Opal services is provided by Axis, e.g.
> http://ws.nbcr.net/opal2/services. Does that not work for you?
> 
> Cheers,
> Sriram
> 
> On Oct 4, 2010, at 9:16 AM, Daniel Blezek wrote:
> 
>>  Hi,
>>  
>>    We¹re using Taverna ( http://www.taverna.org.uk/) as our workflow engine,
>> and would like to expose some of our command line apps.  I was able to
>> connect to the getVersion service.  When I tried to install the date service,
>> I get this error (in the tomcat log):
>>  
>>  Oct 4, 2010 11:10:06 AM org.apache.catalina.core.StandardWrapperValve invoke
>>  SEVERE: Servlet.service() for servlet [AxisServlet] in context with path
>> [/opal2] threw exce
>>  ption [Servlet execution threw an exception] with root cause
>>  java.lang.NoClassDefFoundError: Could not initialize class
>> edu.sdsc.nbcr.opal.AppServiceImpl
>>      at java.lang.Class.forName0(Native Method)
>>      at java.lang.Class.forName(Class.java:247)
>>  <snip>
>>  
>>  And the List page doesn¹t show any services.
>>  
>>  I also can¹t connect to the dashboard:
>>  
>>  java.lang.NoClassDefFoundError: Could not initialize class
>> edu.sdsc.nbcr.opal.state.HibernateUtil
>>   
>> edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:73)
>>   
>> edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.jav
>> a:109)
>>   
>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:108)
>>  
>>  
>>  Any help?
>>  
>>  Also: is there some way to publish all the services on one URL so Taverna
>> will grab all of them rather than one at a time?
>>  
>>  Thanks,
>>  -dan
>>  
>>  -- 
>>  Daniel Blezek, PhD
>>  Medical Imaging Informatics Innovation Center
>>  
>>  P 127 or (77) 8 8886
>>  T 507 538 8886
>>  E ble...@ma...
>>  
>>  Mayo Clinic
>>  200 First St. S.W.
>>  Harwick SL-44
>>  Rochester, MN 55905
>>  mayoclinic.org
>>  "It is more complicated than you think." -- RFC 1925
>>   
>>   
>> 
----------------------------------------------------------------------------->>
-
>> Virtualization is moving to the mainstream and overtaking non-virtualized
>> environment for deploying applications. Does it make network security
>> easier or more difficult to achieve? Read this whitepaper to separate the
>> two and get a better understanding.
>> http://p.sf.net/sfu/hp-phase2-d2d____________________________________________
>> ___
>> Opaltoolkit-users mailing list
>> Opa...@li...
>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
> 
> 

-- 
Daniel Blezek, PhD
Medical Imaging Informatics Innovation Center

P 127 or (77) 8 8886
T 507 538 8886
E ble...@ma...

Mayo Clinic
200 First St. S.W.
Harwick SL-44
Rochester, MN 55905
mayoclinic.org
"It is more complicated than you think." -- RFC 1925

Re: [Opaltoolkit-users] Installation problems

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

Hi Daniel,

It appears as if none of the Opal jars can be found. Did you restart  
Tomcat after Opal installation? At this point, Opal can't be hot- 
deployed, and you will have to restart your Tomcat after installation.  
If you have indeed restarted, please check your CATALINA_HOME/webapps/ 
opal2/WEB-INF/lib to see if all the Opal jars are present. If they  
aren't, something went wrong with the installation.

A list of Opal services is provided by Axis, e.g. http://ws.nbcr.net/opal2/services 
. Does that not work for you?

Cheers,
Sriram

On Oct 4, 2010, at 9:16 AM, Daniel Blezek wrote:

> Hi,
>
>   We’re using Taverna ( http://www.taverna.org.uk/) as our workflow  
> engine, and would like to expose some of our command line apps.  I  
> was able to connect to the getVersion service.  When I tried to  
> install the date service, I get this error (in the tomcat log):
>
> Oct 4, 2010 11:10:06 AM  
> org.apache.catalina.core.StandardWrapperValve invoke
> SEVERE: Servlet.service() for servlet [AxisServlet] in context with  
> path [/opal2] threw exce
> ption [Servlet execution threw an exception] with root cause
> java.lang.NoClassDefFoundError: Could not initialize class  
> edu.sdsc.nbcr.opal.AppServiceImpl
>     at java.lang.Class.forName0(Native Method)
>     at java.lang.Class.forName(Class.java:247)
> <snip>
>
> And the List page doesn’t show any services.
>
> I also can’t connect to the dashboard:
>
> java.lang.NoClassDefFoundError: Could not initialize class  
> edu.sdsc.nbcr.opal.state.HibernateUtil
>   
> edu 
> .sdsc 
> .nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:73)
>   
> edu 
> .sdsc 
> .nbcr 
> .opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:109)
>   
> org 
> .apache 
> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:108)
>
>
> Any help?
>
> Also: is there some way to publish all the services on one URL so  
> Taverna will grab all of them rather than one at a time?
>
> Thanks,
> -dan
>
> -- 
> Daniel Blezek, PhD
> Medical Imaging Informatics Innovation Center
>
> P 127 or (77) 8 8886
> T 507 538 8886
> E ble...@ma...
>
> Mayo Clinic
> 200 First St. S.W.
> Harwick SL-44
> Rochester, MN 55905
> mayoclinic.org
> "It is more complicated than you think." -- RFC 1925
> ------------------------------------------------------------------------------
> Virtualization is moving to the mainstream and overtaking non- 
> virtualized
> environment for deploying applications. Does it make network security
> easier or more difficult to achieve? Read this whitepaper to  
> separate the
> two and get a better understanding.
> http://p.sf.net/sfu/hp-phase2-d2d_______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

[Opaltoolkit-users] Installation problems

[Daniel B. <Ble...@ma...>]

Hi,

  We¹re using Taverna ( http://www.taverna.org.uk/) as our workflow engine,
and would like to expose some of our command line apps.  I was able to
connect to the getVersion service.  When I tried to install the date
service, I get this error (in the tomcat log):

Oct 4, 2010 11:10:06 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [AxisServlet] in context with path
[/opal2] threw exce
ption [Servlet execution threw an exception] with root cause
java.lang.NoClassDefFoundError: Could not initialize class
edu.sdsc.nbcr.opal.AppServiceImpl
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:247)
<snip>

And the List page doesn¹t show any services.

I also can¹t connect to the dashboard:

java.lang.NoClassDefFoundError: Could not initialize class
edu.sdsc.nbcr.opal.state.HibernateUtil
 edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:73
)
 edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.j
ava:109)
 org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:10
8)


Any help?

Also: is there some way to publish all the services on one URL so Taverna
will grab all of them rather than one at a time?

Thanks,
-dan

-- 
Daniel Blezek, PhD
Medical Imaging Informatics Innovation Center

P 127 or (77) 8 8886
T 507 538 8886
E ble...@ma...

Mayo Clinic
200 First St. S.W.
Harwick SL-44
Rochester, MN 55905
mayoclinic.org
"It is more complicated than you think." -- RFC 1925

[Opaltoolkit-users] Opal Toolkit Version 2.3.1 Released

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

We are pleased to announce the release of version 2.3.1 of the Opal  
Toolkit. Version 2.3.1 is a bug fix release, and addresses some issues  
with version 2.3.

Bug fixes include:
   - Uploading of files in for non-mutually exclusive groups on the  
auto-generated forms
   - Ability to copy attachments across different partitions
   - Opal SOAP filter for typed services
     * Failure of generic Opal command-line client while uploading  
input files
     * Interoperability with Axis2 MTOM WSDL2Java clients

If you are affected by any of the bugs above, you are encouraged to  
upgrade to version 2.3.1. If not, you may continue to use version 2.3.

Opal 2.3.1 can be downloaded from here: https://sourceforge.net/projects/opaltoolkit/files/

Sincerely,
Opal Team

[Opaltoolkit-users] Opal Toolkit Version 2.3 Released!

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

We are pleased to announce the release of version 2.3 of the Opal  
Toolkit.

New features in the 2.3 release of Opal include:
   - Direct support for TORQUE/PBS without the need for DRMAA or Globus
   - Limits for the Fork job manager for the number of jobs that can  
be executed concurrently
   - Support for upload of tarballs and zip files for inputs, which  
can be expanded on the server side
   - Support for user email as an optional argument for job tracking
   - Simplification of the input forms with the removal of number of  
CPUs for non-parallel jobs
   - Support for the dynamic addition of multiple file uploads on  
simple form
   - Modification of jobID to include service name
   - Refreshed look and feel for the Opal dashboard (more details on  
the CHANGELOG)

Bug fixes include:
   - The destroy() operation, where baseURL was incorrectly returned  
as empty after job destruction
   -  IP limits, where the query for filtering by IP was incorrect
   -  Opal GUI timeout error for simple form, which returned a stack  
trace on timeout
   -  SOAP filter for automatic WSDL generation/translation to now  
support large files and for empty arguments correctly
   -  Automatic interface UI issues related to radio buttons and  
mutual exclusion

Opal 2.3 can be downloaded from here: https://sourceforge.net/projects/opaltoolkit/files/

Sincerely,
Opal Team

Re: [Opaltoolkit-users] Opal DRMAA with Torque

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

Hi Peter,

We have never had any luck getting DRMAA to work with PBS/Torque. The  
DRMAA implementation has only really been tested using SGE.

However, we now have a new PBSJobManager in SVN. If you can wait till  
around mid May, we are planning on a next release which will include  
this job manager - and some documentation for the same. If you would  
like to try it out beforehand, just update from SVN (and let us know  
if you have any comments). To use it, simply set opal.jobmanager to  
edu.sdsc.nbcr.opal.manager.PBSJobManager in your opal.properties. You  
also have to make sure that all of the Torque commands like qsub,  
qstat, etc are in your path before you restart Tomcat.

Cheers,
Sriram

On Apr 19, 2010, at 7:24 PM, Peter Scott wrote:

> Hi Opal Users,
>
> I am  trying to get Opal working as part of the Meme Suite. I am  
> trying to use Opal to dispatch jobs to our cluster running Torque  
> PBS using DRMAA.
> I believe that the Torque implementation of DRMAA differs from the  
> SGE implementation, especially concerning the return value of  
> drmaa_wait().
> With Torque this causes errors even with the Torque DRMAA build test  
> code (described in OGF DRMAA v 1.0 - PBS/Torque Experience).
> I suspect that that the return value is preventing completion of the  
> job and am starting to look at hacking away at the Torque DRMAA  
> source code.
> One alternative that I see is to use Globus instead of DRMAA however  
> this would require an overhaul of the cluster infrastructure and  
> strikes me as a heavy handed approach. Another option would be to  
> write a new job interface using the Opal libs but ideally I would  
> like to use the native Opal DRMAA interface.
> Does anyone have any experience getting Opal to dispatch jobs to PBS  
> Torque (We are using Maui as the scheduler) ?
> Can anyone advise on how the DRMAA interface is implemented within  
> Opal (what parameters are passed to DRMAA and where they come from  
> etc).
>
> Regards,
>
> Peter Scott
>
> Peter Scott
> Queensland Facility for Advanced Bioinformatics
> Institute for Molecular Bioscience
> Queensland Bioscience Precinct
> University of Queensland
> St Lucia QLD 4072
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

[Opaltoolkit-users] Opal DRMAA with Torque

[Peter S. <p.s...@uq...>]

Hi Opal Users,
 
I am  trying to get Opal working as part of the Meme Suite. I am trying
to use Opal to dispatch jobs to our cluster running Torque PBS using
DRMAA.
I believe that the Torque implementation of DRMAA differs from the SGE
implementation, especially concerning the return value of drmaa_wait().
With Torque this causes errors even with the Torque DRMAA build test
code (described in OGF DRMAA v 1.0 - PBS/Torque Experience).
I suspect that that the return value is preventing completion of the job
and am starting to look at hacking away at the Torque DRMAA source code.
One alternative that I see is to use Globus instead of DRMAA however
this would require an overhaul of the cluster infrastructure and strikes
me as a heavy handed approach. Another option would be to write a new
job interface using the Opal libs but ideally I would like to use the
native Opal DRMAA interface.
Does anyone have any experience getting Opal to dispatch jobs to PBS
Torque (We are using Maui as the scheduler) ?
Can anyone advise on how the DRMAA interface is implemented within Opal
(what parameters are passed to DRMAA and where they come from etc).
 
Regards,
 
Peter Scott
 
Peter Scott
Queensland Facility for Advanced Bioinformatics
Institute for Molecular Bioscience
Queensland Bioscience Precinct
University of Queensland
St Lucia QLD 4072
 

Re: [Opaltoolkit-users] Need A help

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

A couple of other comments -

* Did you start Tomcat? I am not certain from your email whether you  
did or not. If not, you might want to run Tomcat using their startup  
scripts ($CATALINA_HOME/bin/startup.sh)

* You will have to run "ant install" from the Opal installation  
directory - that is where the build.xml exists.

Sriram

On Mar 31, 2010, at 1:35 PM, Jane Ren wrote:

> Hi Ranjan,
>
> I think everything failed because ant complained build.xml didn't  
> exist.
> Did you not run "ant install" from the Opal home directory?
>
> Jane
> ________________________________________
> From: Ranjan Sarmah [sar...@gm...]
> Sent: Wednesday, March 31, 2010 3:16 AM
> To: opa...@li...
> Subject: [Opaltoolkit-users] Need A help
>
> Dear Sir,
>  I have mention the details what I have done till now.
> 1.I have installed ROCKS5.2 in my sun fire  
> X4440(www.rocksclusters.org<http://www.rocksclusters.org/>)
> 2. I have installed "jdk 1.5" and then install "apache ant" and  
> after that i have set the environment variable in /etc/profile at  
> the bottom as
> export ANT_HOME=/usr/local/ant/
> apache-ant-1.7.1
> export JAVA_HOME=/opt/java/jdk1.5
> export PATH= $JAVA_HOME/bin:$ANT_HOME/bin:$PATH
>
> after that i have seen the "java -version"  and "ant -version".
> There i have noticed that java -version is shown correctly but in  
> case of ant it shows that build.xml does not exits.
> Next I move to install apache tomcat. It has been installed. but  
> when I check it in the browser by typing http://localhost:8080<http://localhost:8080/ 
> > . but nothing is coming. I have set the environment variable in  
> the /etc/profile as
> export CATALINA_HOME=/opt/tomcat
> Now Sir what should I have to do? Can you please sent me the details  
> of installation of java, ant and tomcat and also the environment  
> variable to be set. It is must needed for me. I hope you will help  
> me out.
>
> With Regards
> Ranjan Sarmah
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

Re: [Opaltoolkit-users] Need A help

[Jane R. <j2...@uc...>]

Hi Ranjan,

I think everything failed because ant complained build.xml didn't exist.
Did you not run "ant install" from the Opal home directory?

Jane
________________________________________
From: Ranjan Sarmah [sar...@gm...]
Sent: Wednesday, March 31, 2010 3:16 AM
To: opa...@li...
Subject: [Opaltoolkit-users] Need A help

Dear Sir,
  I have mention the details what I have done till now.
1.I have installed ROCKS5.2 in my sun fire X4440(www.rocksclusters.org<http://www.rocksclusters.org/>)
2. I have installed "jdk 1.5" and then install "apache ant" and after that i have set the environment variable in /etc/profile at the bottom as
export ANT_HOME=/usr/local/ant/
apache-ant-1.7.1
export JAVA_HOME=/opt/java/jdk1.5
export PATH= $JAVA_HOME/bin:$ANT_HOME/bin:$PATH

after that i have seen the "java -version"  and "ant -version".
There i have noticed that java -version is shown correctly but in case of ant it shows that build.xml does not exits.
Next I move to install apache tomcat. It has been installed. but when I check it in the browser by typing http://localhost:8080<http://localhost:8080/> . but nothing is coming. I have set the environment variable in the /etc/profile as
export CATALINA_HOME=/opt/tomcat
Now Sir what should I have to do? Can you please sent me the details of installation of java, ant and tomcat and also the environment variable to be set. It is must needed for me. I hope you will help me out.

With Regards
Ranjan Sarmah

[Opaltoolkit-users] Need A help

[Ranjan S. <sar...@gm...>]

Dear Sir,
  I have mention the details what I have done till now.
1.I have installed ROCKS5.2 in my sun fire X4440(www.rocksclusters.org)
2. I have installed "jdk 1.5" and then install "apache ant" and after that i
have set the environment variable in /etc/profile at the bottom as
export ANT_HOME=/usr/local/ant/
apache-ant-1.7.1
export JAVA_HOME=/opt/java/jdk1.5
export PATH= $JAVA_HOME/bin:$ANT_HOME/bin:$PATH

after that i have seen the "java -version"  and "ant -version".
There i have noticed that java -version is shown correctly but in case of
ant it shows that build.xml does not exits.
Next I move to install apache tomcat. It has been installed. but when I
check it in the browser by typing http://localhost:8080 . but nothing is
coming. I have set the environment variable in the /etc/profile as
export CATALINA_HOME=/opt/tomcat
Now Sir what should I have to do? Can you please sent me the details of
installation of java, ant and tomcat and also the environment variable to be
set. It is must needed for me. I hope you will help me out.

With Regards
Ranjan Sarmah

Re: [Opaltoolkit-users] Need A help

[Ranjan S. <sar...@gm...>]

Dear Sir,
 I do have a sun server (sun fire x4440) where I have installed ROCKS 5.2
and now i want to install meme.But before installing meme I have to install
Opal.But I have seen that before going to install OPAL it is adviced to
install JAVA and ANT.I have installed the JAVA and ANT, but I found
something problem in the setting of environment variable of JAVA_HOME and
ANT_HOME.
  Sir, can you please tell me actually where I have to set the environment
variable of JAVA_HOME and ANT_HOME and what is to written there? I am using
bash shell. I will be extremely thankful if you help me to come out of this
problem.



With Regards
Ranjan Sarmah
AAU, Jorhat

Re: [Opaltoolkit-users] Opal-perl for Opal2?

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

Hello Doug,

The APIs are backwards compatible for the most part - so you should be  
able to use version 1.9.2 against the latest version of the Opal2  
server. However, it doesn't take advantage of some of the performance  
improvements - in particular, the support for MIME attachments to  
upload files.

We would like to add support for the new features into opal-perl in  
the future - however, it wasn't very high on our list of priorities  
because no one asked for it :). If you would like to contribute to it,  
you are more than welcome. Meanwhile, we will put it on our list of  
things to do as well.

Thanks,
Sriram

On Mar 26, 2010, at 11:37 AM, Jennewein, Douglas M wrote:

> Is there any plan to add support for Opal2 to opal-perl?  It looks  
> like the latest version is 1.9.2.
>
>
> Doug Jennewein
> Research Analyst
> Department of Computer Science
> University of South Dakota
> Vermillion, SD 57069
> (605) 677-5388
> (605) 677-6662 (fax)
> Dou...@us...
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

[Opaltoolkit-users] Opal-perl for Opal2?

[Jennewein, D. M <Dou...@us...>]

Is there any plan to add support for Opal2 to opal-perl?  It looks like the latest version is 1.9.2.


Doug Jennewein
Research Analyst
Department of Computer Science
University of South Dakota
Vermillion, SD 57069
(605) 677-5388
(605) 677-6662 (fax)
Dou...@us...<mailto:Dou...@us...>

[Opaltoolkit-users] Opal Python (opal-py) Version 2.2 Released

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

Dear all,

We are pleased to announce the release of version 2.2 of the Opal  
Python (opal-py) client. This release corresponds to the latest  
release of the Opal Java core implementation.

Opal-py 2.2 now contains a generic Python client with the same  
functionality as the corresponding Java client. It also includes  
updated documentation for the same.

Opal-py 2.2 can be downloaded from: https://sourceforge.net/projects/opaltoolkit/files 
.

More information about the Opal Toolkit, including relevant  
documentation, can be found at: http://opal.nbcr.net.

Sincerely,
Opal Team

Re: [Opaltoolkit-users] Preferred method retrieving output files in Opal service client scripts

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

Hi Charles,

The getOutputAsBase64ByName() is mostly there for legacy purposes.  
When files are transported as Base64 encoded binary between client and  
server, they are loaded into memory by the server. We noticed that  
this caused the server to get extremely sluggish - the preferred  
approach is now to use MIME attachments for file uploads, and regular  
HTTP downloads the way you are using right now.

That said, you need a job id and a file name to use the above method.  
Blocking jobs typically don't return a job ID, but you can get the ID  
from the baseURL (it is everything after the last "/" - of the form  
"app...").

Thanks,
Sriram

On Feb 8, 2010, at 5:40 PM, Charles Grant wrote:

> Hi,
>
> I'm using the Pdb2pqrClient.py and pdb2pqrclient.pl scripts as  
> templates for writing scripts that submit jobs to the MEME Opal  
> service. I notice that those scripts contain commented out code for  
> retrieving the output files using getOutputAsBase64ByName(). I was  
> able to take that code and extend it to retrieve all the output  
> files for a MEME job that had been submitted as a polling job.  
> However it didn't seem to work for a blocking job. The return value  
> for a blocking job doesn't seem to explicitly contain the jobID  
> value seems to be needed to build the request object for the call to  
> getOutputAsBase64ByName(). However, I am able to retrieve the output  
> files for both polling and blocking jobs using urllib and the urls  
> returned in the _outputFile array.
>
> Are there reasons for preferring getOutputAsBase64ByName() over say,  
> urllib.FancyURLopener()/read()? If so is there a way to call  
> getOutputAsBase64ByName() after a blocking job?
>
>
> Thanks,
>
> Charles
>
>
>
> ------------------------------------------------------------------------------
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[Opaltoolkit-users] Preferred method retrieving output files in Opal service client scripts

[Charles G. <cegrant@u.washington.edu>]

Hi,

I'm using the Pdb2pqrClient.py and pdb2pqrclient.pl scripts as templates for writing scripts that submit jobs to the MEME Opal service. I notice that those scripts contain commented out code for retrieving the output files using getOutputAsBase64ByName(). I was able to take that code and extend it to retrieve all the output files for a MEME job that had been submitted as a polling job. However it didn't seem to work for a blocking job. The return value for a blocking job doesn't seem to explicitly contain the jobID value seems to be needed to build the request object for the call to getOutputAsBase64ByName(). However, I am able to retrieve the output files for both polling and blocking jobs using urllib and the urls returned in the _outputFile array.

Are there reasons for preferring getOutputAsBase64ByName() over say, urllib.FancyURLopener()/read()? If so is there a way to call getOutputAsBase64ByName() after a blocking job?


Thanks,

Charles

Re: [Opaltoolkit-users] Problem installing Opal 2.X

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

No problem Conrad. Glad to hear that our software is of use to you guys.

Cheers,
Sriram

On Feb 8, 2010, at 6:19 PM, Conrad Huang wrote:

> Sorry about the false alarm.  The whole thing is my fault because I  
> installed Opal2 as user "root".  The installed tree was not writable  
> by the tomcat server, hence the error.  Reinstalling as the correct  
> user fixed everything.  Thank you for your help and the great  
> software.
>
> Conrad
>
> On 2/4/10 4:59 PM, Sriram Krishnan wrote:
>> Note that version 1.9.5 didn't use Hibernate and HSQL - all Opal  
>> state
>> was stored in memory, which was lost when Tomcat was restarted.
>>
>> The HSQL files should be in $CATALINA_HOME/webapps/opal2/WEB-INF/ 
>> data/.
>> Does that exist for you?
>>
>> A good test would be install this in a fresh version of Tomcat. I  
>> just
>> downloaded an Opal installation from SourceForge and installed it  
>> inside
>> a fresh version of Tomcat 5.5.28, and did the exact same changes you
>> did, and everything worked fine. It is possible that there may be  
>> some
>> conflicts with other web applications deployed inside your Tomcat
>> instance. If you can't get Opal installed on a vanilla fresh  
>> Tomcat, we
>> can help you debug that.
>>
>> Thanks,
>> Sriram
>>
>> On Feb 4, 2010, at 4:31 PM, Conrad Huang wrote:
>>
>>> I did not touch etc/hibernate-opal.cfg.xml. The only two files from
>>> the standard 2.2 distribution that I modified were etc/ 
>>> opal.properties
>>> and build.properties. In opal.properties, the only item I changed  
>>> was
>>> "tomcat.url", which I set to be the same as on 1.9.5. The
>>> build.properties file for 1.9.5 and 2.2 are the same except for
>>> "version".
>>>
>>> I guess I'm unclear on where the HSQL databases are for 1.9.5 and  
>>> 2.2
>>> are. On 1.9.5, in etc/opal.properties, I have
>>>
>>> database.use=false
>>>
>>> On 2.2, in etc/hibernate-opal.cfg.xml, I have
>>>
>>> <property name="connection.url">jdbc:hsqldb:file:data/opaldb</ 
>>> property>
>>>
>>> Where on the file system should these databases live, given these
>>> settings?
>>>
>>> Thanks.
>>>
>>> Conrad
>>>
>>> On 2/4/10 4:08 PM, Sriram Krishnan wrote:
>>>> Hi Conrad,
>>>>
>>>> Just to elaborate on Jane's question - did you modify the
>>>> etc/hibernate-opal.cfg.xml as well? I would recommend default the
>>>> default configuration (i.e. using the HSQL database) first, and  
>>>> checking
>>>> if everything works out of the box.
>>>>
>>>> Once that works, you can try connecting to another database. Also  
>>>> note
>>>> that the database schemas for Opal 1.9.5 and Opal 2.X are  
>>>> different. So
>>>> if you are using the same database instance, please use a different
>>>> database name in the "connection.url".
>>>>
>>>> Let us know if that helps.
>>>> Sriram
>>>>
>>>> On Feb 4, 2010, at 3:19 PM, Jane Ren wrote:
>>>>
>>>>> Hi Conrad,
>>>>>
>>>>> Are you using the default database?
>>>>>
>>>>> Jane
>>>>> ________________________________________
>>>>> From: Conrad Huang [co...@cg...]
>>>>> Sent: Thursday, February 04, 2010 2:34 PM
>>>>> To: opa...@li...
>>>>> Subject: [Opaltoolkit-users] Problem installing Opal 2.X
>>>>>
>>>>> I've been using Opal 1.9.5 for a while and it works very well  
>>>>> for us.
>>>>> Now that 2.2 is out, I'd like to migrate to the newer version  
>>>>> while
>>>>> keeping the old one up and running for legacy users. Following the
>>>>> instructions, I managed to get through "edit etc/opal.properties  
>>>>> and
>>>>> build.properties" and "ant install", but starting tomcat at that  
>>>>> point
>>>>> generates the attached error log. The old 1.9.5 services are  
>>>>> working
>>>>> fine, but services deployed for 2.2 generate similar exceptions  
>>>>> about
>>>>> "Connections could not be acquired from the underlying  
>>>>> database!" Can
>>>>> someone please point me towards where I went wrong? Thanks.
>>>>>
>>>>> Conrad
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>>
>>>>>
>>>>> The Planet: dedicated and managed hosting, cloud storage,  
>>>>> colocation
>>>>> Stay online with enterprise data centers and the best network in  
>>>>> the
>>>>> business
>>>>> Choose flexible plans and management services without long-term
>>>>> contracts
>>>>> Personal 24x7 support from experience hosting pros just a phone  
>>>>> call
>>>>> away.
>>>>> http://p.sf.net/sfu/theplanet-com
>>>>> _______________________________________________
>>>>> Opaltoolkit-users mailing list
>>>>> Opa...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>>>
>>