gridsam-discuss — GridSAM users and developers

Re: [gridsam-discuss] The Java API Tutorial

[John S. R. <J.S...@so...>]

Hi Richard,

Sounds like a namespace issue.  Your attachments seemed to have been
stripped by the list.  Could post your JSDL / logs to pastebin or to me
directly, please?

Cheers,

John Robinson

On Fri, 2011-09-23 at 11:14 +0100, Richard Kavanagh wrote:
> Hello,
> 
> I've been trying to follow the Java API Tutorial (http://www.omii.ac.uk/docs/3.4.0/training_guide/tutorial_3/gridsam_java_api_tutorial.htm) however the result is that I get the following submission exception:
> 
> Exception in thread "main" org.icenigrid.gridsam.core.SubmissionException: failed to submit job: No jsdl:JobDefinition element can be found in the request. Please check your input and the namespace declarations.
>         at org.icenigrid.gridsam.client.common.ClientSideJobManager.submitJob(ClientSideJobManager.java:302)
>         at org.icenigrid.gridsam.client.common.ClientSideJobManager.submitJob(ClientSideJobManager.java:327)
>         at gridsamapitesting.GSExample.main(GSExample.java:34)
> Caused by: javax.xml.rpc.ServiceException: No jsdl:JobDefinition element can be found in the request. Please check your input and the namespace declarations.
>         at org.icenigrid.gridsam.client.common.GridSAMClientSupport.submitJob(GridSAMClientSupport.java:193)
>         at org.icenigrid.gridsam.client.common.ClientSideJobManager.submitJob(ClientSideJobManager.java:285)
>         ... 2 more
> 
> Is there any guidance you could offer me? I am attaching several logs that may be of interest and detail the error further. I've managed to run the demo scripts such as primes_file and fractal_ftp without issue, so I can conclude the installation as a whole works and that I can't be too far away from making the java api work as well.
> 
> Thanks in advance,
> 
> Richard.
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2dcopy2
> _______________________________________________ GridSAM-Discuss mailing list Gri...@li... https://lists.sourceforge.net/lists/listinfo/gridsam-discuss

-- 

John S. Robinson 
Senior Software Consultant
School of Electronics & Computer Science 
University of Southampton, SO17 1BJ, UK 
J.S...@so...

Re: [gridsam-discuss] Problem using gridFTP

[Ismael M. C. <i....@fd...>]

Thanks for your help. 

Changing the logging level (to DEBUG), the problem seems disappear. I
have performed several executions and not crash, but when I turn to set
the logging level to INFO , the problem appears after only one or two
executions. I guess that any sentence causes the problem when INFO
debugging is set.
  
On Wed, 2011-03-09 at 13:28 +0000, Justin Bradley wrote:
> Hi Ismael, 
> 
> Just to check, but have you run grid-proxy-init from your GridSAM's user account?
> 
> It might be useful to up the logging level on GridSAM too, may give us a better idea as to what it happening.
> ( webapps/gridsam/WEB-INF/classes/log4j.properties )  By default its set to INFO rather than DEBUG.
> 
> Googling gave me this http://lists.globus.org/pipermail/workspace-user/2010-July/001358.html
> Its the same error you are getting, although may not be the same problem, its worth having a quick read.
> 
> 	Justin
> 
> On 9 Mar 2011, at 13:01, Ismael Marín Carrión wrote:
> 
> > Hi Justin,
> > 
> > 
> > On Wed, 2011-03-09 at 12:05 +0000, Justin Bradley wrote:
> >> Hi,
> >> 
> >> 
> >> Do you have access to the gridFTP server logs, if so do they give any
> >> more detail?
> > 
> > Yes, but it does not provide any error when connexion is broken.
> > 
> >> Also, how are you authenticating with the gridFTP server?
> >> 
> > I use a myproxy server for authenticating. In the JSDL, I provide the
> > server, port and, user and passwd needed for it.
> >> 
> >> Regards,
> >> Justin
> >> 
> >> On 9 Mar 2011, at 09:06, Ismael Marín Carrión wrote:
> >> 
> >>> Dear all,
> >>> 
> >>> I'm getting a random error when I use gridFTP for data staging-out.
> >>> The gridFTP is running as standalone (daemon flag is activated) and
> >>> version is 3.23.
> >>> 
> >>> The error stack is:
> >>> 
> >>> 2011-03-09 09:45:44,099 INFO  [job] ff8080812e99ca64012e99caad8a0001
> >>> reason for failure: Unknown message with code "Unknown message with
> >>> code "Unknown message with code "Unknown message with code "Unknown
> >>> message with code "Server refused performing the request. Custom
> >>> message:  (error code 1) [Nested exception message:  Custom message:
> >>> Unexpected reply: 451 active connection to server failed
> >>> java.net.ConnectException: Connection refused
> >>> java.net.ConnectException: Connection refused
> >>> at java.net.PlainSocketImpl.socketConnect(Native Method)
> >>> at
> >>> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
> >>> at
> >>> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
> >>> at
> >>> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
> >>> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
> >>> at java.net.Socket.connect(Socket.java:546)
> >>> at java.net.Socket.connect(Socket.java:495)
> >>> at java.net.Socket.<init>(Socket.java:392)
> >>> at java.net.Socket.<init>(Socket.java:293)
> >>> at org.globus.net.SocketFactory.createSocket(SocketFactory.java:74)
> >>> at org.globus.net.SocketFactory.createSocket(SocketFactory.java:53)
> >>> at
> >>> org.globus.ftp.dc.GridFTPActiveConnectTask.execute(GridFTPActiveConnectTask.java:70)
> >>> at org.globus.ftp.dc.TaskThread.run(TaskThread.java:71)
> >>> at java.lang.Thread.run(Thread.java:636)
> >>> ]".".".".".
> >>> 
> >>> This not happens using globus-url-copy client or even other
> >>> java-based clients making use of jglobus (1.6 and 1.8). No problems
> >>> were found with a batch of 400 requests (with a level of concurrency
> >>> of 2 requests). Also, the server uses a limited range of ports,
> >>> while the client uses any free port. Thus, I guess that some in the
> >>> implementation of GridSAM causes this problem.
> >>> 
> >>> Moreover, tracking the code, GridSAM 2.3 is using:
> >>> 
> >>> import uk.ac.nesc.vfs.gsiftp.GSIFTPFileProvider;
> >>> import uk.ac.nesc.vfs.gsiftp.GSIFTPFileSystemConfigBuilder;
> >>> 
> >>> and not the similar classes on
> >>> org.icenigrid.gridsam.core.plugin.vfs.gsiftp.*. Using these last
> >>> classes GridSam crashes before of establishing a connexion with the
> >>> gridFTP server.
> >>> 
> >>> Therefore, Could you tell me some workaround for this? or What is
> >>> version/s of gridFTP tested with GridSam? and eventually, Could I
> >>> download the java package uk.ac.nesc.vfs.gsiftp?
> >>> 
> >>> Best regards and thanks in advance.
> >>> ------------------------------------------------------------------------------
> >>> Colocation vs. Managed Hosting
> >>> A question and answer guide to determining the best fit
> >>> for your organization - today and in the future.
> >>> http://p.sf.net/sfu/internap-sfd2d_______________________________________________
> >>> GridSAM-Discuss mailing list
> >>> Gri...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss
> >> 
> >> --
> >> Justin Bradley
> >> Senior Software Consultant
> >> jb...@ec...
> >> ECS / EPrints Services / SSI
> >> Bay 22, 4067, B32
> >> University of Southampton
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> ------------------------------------------------------------------------------
> >> Colocation vs. Managed Hosting
> >> A question and answer guide to determining the best fit
> >> for your organization - today and in the future.
> >> http://p.sf.net/sfu/internap-sfd2d
> >> _______________________________________________ GridSAM-Discuss mailing list Gri...@li... https://lists.sourceforge.net/lists/listinfo/gridsam-discuss
> > 
> > 
> 
> --
> Justin Bradley
> Senior Software Consultant
> jb...@ec...
> ECS / EPrints Services / SSI
> Bay 22, 4067, B32
> University of Southampton
> 
> 
> 
> 
> 

Re: [gridsam-discuss] Problem using gridFTP

[Justin B. <jb...@ec...>]

Hi Ismael, 

Just to check, but have you run grid-proxy-init from your GridSAM's user account?

It might be useful to up the logging level on GridSAM too, may give us a better idea as to what it happening.
( webapps/gridsam/WEB-INF/classes/log4j.properties )  By default its set to INFO rather than DEBUG.

Googling gave me this http://lists.globus.org/pipermail/workspace-user/2010-July/001358.html
Its the same error you are getting, although may not be the same problem, its worth having a quick read.

	Justin

On 9 Mar 2011, at 13:01, Ismael Marín Carrión wrote:

> Hi Justin,
> 
> 
> On Wed, 2011-03-09 at 12:05 +0000, Justin Bradley wrote:
>> Hi,
>> 
>> 
>> Do you have access to the gridFTP server logs, if so do they give any
>> more detail?
> 
> Yes, but it does not provide any error when connexion is broken.
> 
>> Also, how are you authenticating with the gridFTP server?
>> 
> I use a myproxy server for authenticating. In the JSDL, I provide the
> server, port and, user and passwd needed for it.
>> 
>> Regards,
>> Justin
>> 
>> On 9 Mar 2011, at 09:06, Ismael Marín Carrión wrote:
>> 
>>> Dear all,
>>> 
>>> I'm getting a random error when I use gridFTP for data staging-out.
>>> The gridFTP is running as standalone (daemon flag is activated) and
>>> version is 3.23.
>>> 
>>> The error stack is:
>>> 
>>> 2011-03-09 09:45:44,099 INFO  [job] ff8080812e99ca64012e99caad8a0001
>>> reason for failure: Unknown message with code "Unknown message with
>>> code "Unknown message with code "Unknown message with code "Unknown
>>> message with code "Server refused performing the request. Custom
>>> message:  (error code 1) [Nested exception message:  Custom message:
>>> Unexpected reply: 451 active connection to server failed
>>> java.net.ConnectException: Connection refused
>>> java.net.ConnectException: Connection refused
>>> at java.net.PlainSocketImpl.socketConnect(Native Method)
>>> at
>>> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
>>> at
>>> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
>>> at
>>> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
>>> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
>>> at java.net.Socket.connect(Socket.java:546)
>>> at java.net.Socket.connect(Socket.java:495)
>>> at java.net.Socket.<init>(Socket.java:392)
>>> at java.net.Socket.<init>(Socket.java:293)
>>> at org.globus.net.SocketFactory.createSocket(SocketFactory.java:74)
>>> at org.globus.net.SocketFactory.createSocket(SocketFactory.java:53)
>>> at
>>> org.globus.ftp.dc.GridFTPActiveConnectTask.execute(GridFTPActiveConnectTask.java:70)
>>> at org.globus.ftp.dc.TaskThread.run(TaskThread.java:71)
>>> at java.lang.Thread.run(Thread.java:636)
>>> ]".".".".".
>>> 
>>> This not happens using globus-url-copy client or even other
>>> java-based clients making use of jglobus (1.6 and 1.8). No problems
>>> were found with a batch of 400 requests (with a level of concurrency
>>> of 2 requests). Also, the server uses a limited range of ports,
>>> while the client uses any free port. Thus, I guess that some in the
>>> implementation of GridSAM causes this problem.
>>> 
>>> Moreover, tracking the code, GridSAM 2.3 is using:
>>> 
>>> import uk.ac.nesc.vfs.gsiftp.GSIFTPFileProvider;
>>> import uk.ac.nesc.vfs.gsiftp.GSIFTPFileSystemConfigBuilder;
>>> 
>>> and not the similar classes on
>>> org.icenigrid.gridsam.core.plugin.vfs.gsiftp.*. Using these last
>>> classes GridSam crashes before of establishing a connexion with the
>>> gridFTP server.
>>> 
>>> Therefore, Could you tell me some workaround for this? or What is
>>> version/s of gridFTP tested with GridSam? and eventually, Could I
>>> download the java package uk.ac.nesc.vfs.gsiftp?
>>> 
>>> Best regards and thanks in advance.
>>> ------------------------------------------------------------------------------
>>> Colocation vs. Managed Hosting
>>> A question and answer guide to determining the best fit
>>> for your organization - today and in the future.
>>> http://p.sf.net/sfu/internap-sfd2d_______________________________________________
>>> GridSAM-Discuss mailing list
>>> Gri...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss
>> 
>> --
>> Justin Bradley
>> Senior Software Consultant
>> jb...@ec...
>> ECS / EPrints Services / SSI
>> Bay 22, 4067, B32
>> University of Southampton
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Colocation vs. Managed Hosting
>> A question and answer guide to determining the best fit
>> for your organization - today and in the future.
>> http://p.sf.net/sfu/internap-sfd2d
>> _______________________________________________ GridSAM-Discuss mailing list Gri...@li... https://lists.sourceforge.net/lists/listinfo/gridsam-discuss
> 
> 

--
Justin Bradley
Senior Software Consultant
jb...@ec...
ECS / EPrints Services / SSI
Bay 22, 4067, B32
University of Southampton

Re: [gridsam-discuss] Problem using gridFTP

[Ismael M. C. <i....@fd...>]

Hi Justin,


On Wed, 2011-03-09 at 12:05 +0000, Justin Bradley wrote:
> Hi,
> 
> 
> Do you have access to the gridFTP server logs, if so do they give any
> more detail?

Yes, but it does not provide any error when connexion is broken.
  
> Also, how are you authenticating with the gridFTP server?
> 
I use a myproxy server for authenticating. In the JSDL, I provide the
server, port and, user and passwd needed for it.
> 
> Regards,
> Justin
> 
> On 9 Mar 2011, at 09:06, Ismael Marín Carrión wrote:
> 
> > Dear all,
> > 
> > I'm getting a random error when I use gridFTP for data staging-out.
> > The gridFTP is running as standalone (daemon flag is activated) and
> > version is 3.23.
> > 
> > The error stack is:
> > 
> > 2011-03-09 09:45:44,099 INFO  [job] ff8080812e99ca64012e99caad8a0001
> > reason for failure: Unknown message with code "Unknown message with
> > code "Unknown message with code "Unknown message with code "Unknown
> > message with code "Server refused performing the request. Custom
> > message:  (error code 1) [Nested exception message:  Custom message:
> > Unexpected reply: 451 active connection to server failed
> > java.net.ConnectException: Connection refused
> > java.net.ConnectException: Connection refused
> > at java.net.PlainSocketImpl.socketConnect(Native Method)
> > at
> > java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
> > at
> > java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
> > at
> > java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
> > at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
> > at java.net.Socket.connect(Socket.java:546)
> > at java.net.Socket.connect(Socket.java:495)
> > at java.net.Socket.<init>(Socket.java:392)
> > at java.net.Socket.<init>(Socket.java:293)
> > at org.globus.net.SocketFactory.createSocket(SocketFactory.java:74)
> > at org.globus.net.SocketFactory.createSocket(SocketFactory.java:53)
> > at
> > org.globus.ftp.dc.GridFTPActiveConnectTask.execute(GridFTPActiveConnectTask.java:70)
> > at org.globus.ftp.dc.TaskThread.run(TaskThread.java:71)
> > at java.lang.Thread.run(Thread.java:636)
> > ]".".".".".
> > 
> > This not happens using globus-url-copy client or even other
> > java-based clients making use of jglobus (1.6 and 1.8). No problems
> > were found with a batch of 400 requests (with a level of concurrency
> > of 2 requests). Also, the server uses a limited range of ports,
> > while the client uses any free port. Thus, I guess that some in the
> > implementation of GridSAM causes this problem.
> > 
> > Moreover, tracking the code, GridSAM 2.3 is using:
> > 
> > import uk.ac.nesc.vfs.gsiftp.GSIFTPFileProvider;
> > import uk.ac.nesc.vfs.gsiftp.GSIFTPFileSystemConfigBuilder;
> > 
> > and not the similar classes on
> > org.icenigrid.gridsam.core.plugin.vfs.gsiftp.*. Using these last
> > classes GridSam crashes before of establishing a connexion with the
> > gridFTP server.
> > 
> > Therefore, Could you tell me some workaround for this? or What is
> > version/s of gridFTP tested with GridSam? and eventually, Could I
> > download the java package uk.ac.nesc.vfs.gsiftp?
> > 
> > Best regards and thanks in advance.
> > ------------------------------------------------------------------------------
> > Colocation vs. Managed Hosting
> > A question and answer guide to determining the best fit
> > for your organization - today and in the future.
> > http://p.sf.net/sfu/internap-sfd2d_______________________________________________
> > GridSAM-Discuss mailing list
> > Gri...@li...
> > https://lists.sourceforge.net/lists/listinfo/gridsam-discuss
> 
> --
> Justin Bradley
> Senior Software Consultant
> jb...@ec...
> ECS / EPrints Services / SSI
> Bay 22, 4067, B32
> University of Southampton
> 
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________ GridSAM-Discuss mailing list Gri...@li... https://lists.sourceforge.net/lists/listinfo/gridsam-discuss

Re: [gridsam-discuss] Problem using gridFTP

[Justin B. <jb...@ec...>]

Hi,

Do you have access to the gridFTP server logs, if so do they give any more detail?
Also, how are you authenticating with the gridFTP server?

Regards,
	Justin

On 9 Mar 2011, at 09:06, Ismael Marín Carrión wrote:

> Dear all,
> 
> I'm getting a random error when I use gridFTP for data staging-out. The gridFTP is running as standalone (daemon flag is activated) and version is 3.23.
> 
> The error stack is:
> 
> 2011-03-09 09:45:44,099 INFO  [job] ff8080812e99ca64012e99caad8a0001 reason for failure: Unknown message with code "Unknown message with code "Unknown message with code "Unknown message with code "Unknown message with code "Server refused performing the request. Custom message:  (error code 1) [Nested exception message:  Custom message: Unexpected reply: 451 active connection to server failed
> java.net.ConnectException: Connection refused
> java.net.ConnectException: Connection refused
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
> at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
> at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
> at java.net.Socket.connect(Socket.java:546)
> at java.net.Socket.connect(Socket.java:495)
> at java.net.Socket.<init>(Socket.java:392)
> at java.net.Socket.<init>(Socket.java:293)
> at org.globus.net.SocketFactory.createSocket(SocketFactory.java:74)
> at org.globus.net.SocketFactory.createSocket(SocketFactory.java:53)
> at org.globus.ftp.dc.GridFTPActiveConnectTask.execute(GridFTPActiveConnectTask.java:70)
> at org.globus.ftp.dc.TaskThread.run(TaskThread.java:71)
> at java.lang.Thread.run(Thread.java:636)
> ]".".".".".
> 
> This not happens using globus-url-copy client or even other java-based clients making use of jglobus (1.6 and 1.8). No problems were found with a batch of 400 requests (with a level of concurrency of 2 requests). Also, the server uses a limited range of ports, while the client uses any free port. Thus, I guess that some in the implementation of GridSAM causes this problem.
> 
> Moreover, tracking the code, GridSAM 2.3 is using:
> 
> import uk.ac.nesc.vfs.gsiftp.GSIFTPFileProvider;
> import uk.ac.nesc.vfs.gsiftp.GSIFTPFileSystemConfigBuilder;
> 
> and not the similar classes on org.icenigrid.gridsam.core.plugin.vfs.gsiftp.*. Using these last classes GridSam crashes before of establishing a connexion with the gridFTP server.
> 
> Therefore, Could you tell me some workaround for this? or What is version/s of gridFTP tested with GridSam? and eventually, Could I download the java package uk.ac.nesc.vfs.gsiftp?
> 
> Best regards and thanks in advance.
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d_______________________________________________
> GridSAM-Discuss mailing list
> Gri...@li...
> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss

--
Justin Bradley
Senior Software Consultant
jb...@ec...
ECS / EPrints Services / SSI
Bay 22, 4067, B32
University of Southampton

[gridsam-discuss] Problem using gridFTP

[Ismael M. C. <i....@fd...>]

Dear all,

I'm getting a random error when I use gridFTP for data staging-out. The
gridFTP is running as standalone (daemon flag is activated) and version
is 3.23.

The error stack is:

2011-03-09 09:45:44,099 INFO  [job] ff8080812e99ca64012e99caad8a0001
reason for failure: Unknown message with code "Unknown message with code
"Unknown message with code "Unknown message with code "Unknown message
with code "Server refused performing the request. Custom message:
(error code 1) [Nested exception message:  Custom message: Unexpected
reply: 451 active connection to server failed
java.net.ConnectException: Connection refused
java.net.ConnectException: Connection refused
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at
java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
	at
java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
	at
java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
	at java.net.Socket.connect(Socket.java:546)
	at java.net.Socket.connect(Socket.java:495)
	at java.net.Socket.<init>(Socket.java:392)
	at java.net.Socket.<init>(Socket.java:293)
	at org.globus.net.SocketFactory.createSocket(SocketFactory.java:74)
	at org.globus.net.SocketFactory.createSocket(SocketFactory.java:53)
	at
org.globus.ftp.dc.GridFTPActiveConnectTask.execute(GridFTPActiveConnectTask.java:70)
	at org.globus.ftp.dc.TaskThread.run(TaskThread.java:71)
	at java.lang.Thread.run(Thread.java:636)
]".".".".".

This not happens using globus-url-copy client or even other java-based
clients making use of jglobus (1.6 and 1.8). No problems were found with
a batch of 400 requests (with a level of concurrency of 2 requests).
Also, the server uses a limited range of ports, while the client uses
any free port. Thus, I guess that some in the implementation of GridSAM
causes this problem.

Moreover, tracking the code, GridSAM 2.3 is using:

import uk.ac.nesc.vfs.gsiftp.GSIFTPFileProvider;
import uk.ac.nesc.vfs.gsiftp.GSIFTPFileSystemConfigBuilder;

and not the similar classes on
org.icenigrid.gridsam.core.plugin.vfs.gsiftp.*. Using these last classes
GridSam crashes before of establishing a connexion with the gridFTP
server.

Therefore, Could you tell me some workaround for this? or What is
version/s of gridFTP tested with GridSam? and eventually, Could I
download the java package uk.ac.nesc.vfs.gsiftp?

Best regards and thanks in advance.

[gridsam-discuss] pbs_driver_function_withoutTracejob.sh not working properly

[Pawel S. <paw...@ii...>]

Hello,

I updated to latest GridSAM (2.3.0) and found out that the driver I was 
using (pbs_driver_function_withoutTracejob.sh) started to cause 
problems. Seems like tracking of status was not updated to support lists 
of job ids. I used the pbs_driver_function.sh to fix it and it looks 
like it is working now. It still needs polishing though. You will find a 
diff of the original and fixed file attached.

Regards,
Pawel Sztromwasser

Re: [gridsam-discuss] Environment variables

[Justin B. <jb...@ec...>]

Hi,

Given you don't want to pass environment variables as part of your job description, you may settle on setting them at the GridSAM service level.
You can list the env vars to be passed down to the underlying driver scripts by adding them to the file_driver_environment property in webapps/gridsam/WEB-INF/classes/ICTDRM.properties
There is an additional way to pass environment variables to a job by passing them as soap headers, this may be what you are after.  Or may be in appropriate for the same reasons specifying them in the JDSL is.  This method is achieved by using the KeyValuePair handler detailed in server-config.wsdd and client-config.wsdd.

	Justin




On 23 Feb 2011, at 12:05, Ismael Marín Carrión wrote:

> Dear all, I would like to know how passing/setting environment variables
> by means of GridSam in order to a job can use it. The obvious solution
> of passing the variable in the job description is not valid for our
> case.
> 
> Regards. 
> 
> 
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in 
> Real-Time with Splunk. Collect, index and harness all the fast moving IT data 
> generated by your applications, servers and devices whether physical, virtual
> or in the cloud. Deliver compliance at lower cost and gain new business 
> insights. http://p.sf.net/sfu/splunk-dev2dev 
> _______________________________________________
> GridSAM-Discuss mailing list
> Gri...@li...
> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss

--
Justin Bradley
Senior Software Consultant
jb...@ec...
ECS / EPrints Services / SSI
Bay 22, 4067, B32
University of Southampton

[gridsam-discuss] Environment variables

[Ismael M. C. <i....@fd...>]

Dear all, I would like to know how passing/setting environment variables
by means of GridSam in order to a job can use it. The obvious solution
of passing the variable in the job description is not valid for our
case.

Regards. 

Re: [gridsam-discuss] Problem with AFT

[Ismael M. C. <i....@fd...>]

I let you to know more details. Concretely, 

> at
org.icenigrid.gridsam.core.plugin.transfer.protocol.AbstractTransferAgent.getFileObject(AbstractTransferAgent.java:239)

protected FileObject getFileObject(String url, MyProxyInfo myProxyInfo)
throws IOException
        {
...
                FileObject fileObject = xInstance.resolveFile(url,
createStandardFileSystemOptions(myProxyInfo));
...
}

>  at
org.apache.commons.vfs.impl.DefaultFileSystemManager.resolveFile(DefaultFileSystemManager.java:582)

    public FileObject resolveFile(final String uri,
            final FileSystemOptions fileSystemOptions)
            throws FileSystemException
    {
        // return resolveFile(baseFile, uri, fileSystemOptions);
        return resolveFile(getBaseFile(), uri, fileSystemOptions);
    }

which invokes to:

public FileObject resolveFile(final FileObject baseFile, final String
uri,
            final FileSystemOptions fileSystemOptions)
            throws FileSystemException
    {
        final FileObject realBaseFile;
        if (baseFile != null && VFS.isUriStyle()
                && baseFile.getName().getType() == FileType.FILE)
        {
            realBaseFile = baseFile.getParent();
        }
        else
        {
            realBaseFile = baseFile;
        }
        ...
        // Extract the scheme
        final String scheme = UriParser.extractScheme(uri);
        if (scheme != null)
        {
            final FileProvider provider = providers.get(scheme);
            if (provider != null)
            {
                return provider.findFile(realBaseFile, uri,
fileSystemOptions);
            }
...
}

At this point realBaseFile/baseFile is null, which is not passed from
GridSam classes and causes that the URI be not resolvable. I have tested
different versions of commons-httpclient and commons-vfs. Actually, I am
using commons-vfs 2.1 and commons-httpclient 3.0.1, but similar problems
appear with other versions. Then, Could be a bug? Is well-formed an URL
as  http://localhost:33922//opt/gridway/5.6.1//libexec/gw_wrapper.sh ?
 
Best regards.

On Thu, 2011-01-27 at 10:08 +0100, ISMAEL MARIN CARRION wrote:

> Dear all,
> 
> I have a trouble when I submit a job which uses the transfer AFT file
> job. It uses a GASS (mode insecure) session. There are not problems
> with this session, since I am able to transfer files using the globus
> commands. Below is the log of gridsam.
> 
> 2011-01-27 09:39:40,233 WARN  [UserMappingStage] You disabled security
> features: pool accounts and private workding directory.
> 2011-01-27 09:39:40,241 WARN  [UserMappingStage] Use the local user
> account (root) of gridsam to do jobs for user CN=gridsam
> 2011-01-27 09:39:40,460 INFO  [AbstractFileProviderSupport] SUBMIT Job
> 2011-01-27 09:39:40,481 INFO  [AFTFileTransferJob]  Transfer AFT File
> Job : 3F7944E207B98181095290B8BBF83F4F7839F11F start at 08:39:40
> 481  http://localhost:36199//opt/gridway/5.6.1//libexec/gw_wrapper.sh
> --> /root/workdir/a0/00/46/gridsam-ff8081812dc69192012dc6a0c164000a//opt/gridway/5.6.1//libexec/gw_wrapper.sh.wrapper retry time :0
> 2011-01-27 09:39:40,494 INFO  [HttpMethodBase] Recoverable exception
> caught when processing request
> 2011-01-27 09:39:40,495 WARN  [HttpMethodBase] Recoverable exception
> caught but MethodRetryHandler.retryMethod() returned false, rethrowing
> exception
> 2011-01-27 09:39:40,495 ERROR [TransferAgentFactory] source URI is not
> resolvable
> org.apache.commons.vfs.FileSystemException: Could not connect to HTTP
> server on "localhost".
>     at
> org.apache.commons.vfs.provider.http.HttpClientFactory.createConnection(HttpClientFactory.java:106)
>     at
> org.apache.commons.vfs.provider.http.HttpFileProvider.doCreateFileSystem(HttpFileProvider.java:82)
>     at
> org.apache.commons.vfs.provider.AbstractOriginatingFileProvider.findFile(AbstractOriginatingFileProvider.java:81)
>     at
> org.apache.commons.vfs.provider.AbstractOriginatingFileProvider.findFile(AbstractOriginatingFileProvider.java:62)
>     at
> org.apache.commons.vfs.impl.DefaultFileSystemManager.resolveFile(DefaultFileSystemManager.java:641)
>     at
> org.apache.commons.vfs.impl.DefaultFileSystemManager.resolveFile(DefaultFileSystemManager.java:582)
>     at
> org.icenigrid.gridsam.core.plugin.transfer.protocol.AbstractTransferAgent.getFileObject(AbstractTransferAgent.java:239)
>     at
> org.icenigrid.gridsam.core.plugin.transfer.protocol.TransferAgentFactory.resolveSourceFile(TransferAgentFactory.java:168)
>     at
> org.icenigrid.gridsam.core.plugin.transfer.protocol.TransferAgentFactory.<init>(TransferAgentFactory.java:120)
>     at
> org.icenigrid.gridsam.core.plugin.transfer.provider.AFTFileTransferJob.execute(AFTFileTransferJob.java:131)
>     at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
>     at org.quartz.simpl.SimpleThreadPool
> $WorkerThread.run(SimpleThreadPool.java:525)
> Caused by: org.apache.commons.httpclient.HttpRecoverableException:
> org.apache.commons.httpclient.HttpRecoverableException: Error in
> parsing the status  line from the response: unable to find line
> starting with "HTTP"
>     at
> org.apache.commons.httpclient.HttpMethodBase.readResponse(HttpMethodBase.java:1962)
>     at
> org.apache.commons.httpclient.HttpMethodBase.processRequest(HttpMethodBase.java:2653)
>     at
> org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:1087)
>     at
> org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:643)
>     at
> org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:497)
>     at
> org.apache.commons.vfs.provider.http.HttpClientFactory.createConnection(HttpClientFactory.java:102)
>     ... 11 more
> 2011-01-27 09:39:40,508 INFO  [FileProcessHelper] AFT File
> FAILED.Could not connect to HTTP server on "localhost".
> 2011-01-27 09:39:40,525 INFO  [job] ff8081812dc69192012dc6a0c164000a
> reason for failure: Could not connect to HTTP server on "localhost".
> 2011-01-27 09:39:40,525 INFO  [stats]
> ff8081812dc69192012dc6a0c164000a: pending@1296117580132
> staging-in@1296117580450 failed@1296117580525 
> 2011-01-27 09:39:40,561 INFO  [JobCleanupListener] delete the temp dir
> for failed job ff8081812dc69192012dc6a0c164000a
> 
> 
> The version of commons-httpclient.jar is the 2.0.2, however, I have
> tested other versions with similar results. I hope that someone could
> help me to fix this problem. 
> 
> Best regards.
> 
> ------------------------------------------------------------------------------
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> _______________________________________________ GridSAM-Discuss mailing list Gri...@li... https://lists.sourceforge.net/lists/listinfo/gridsam-discuss

[gridsam-discuss] Parameter Sweeping for GridSAM

[Sanjaya L. <san...@gm...>]

Hi dev,
         I am Sanjaya Liyanage and a final year undergraduate student of the
Department of Computer Science & Engineering,University of Moratuwa.I am
interested in the project idea "Parameter Sweeping for GridSAM" in the 2010
gsoc idea list  and would like to hold it as my this year gsoc project.I am
familiar with java and xml.I would like to contribute the "Parameter
Sweeping for GridSAM" if it will be available in this year Gsoc for
OMII-UK.I am going to start some reading on JSDL this week.Please let me
know your ideas and comments.
 Thank you very much.

Regards,
Sanjaya.

[gridsam-discuss] Problem with AFT

[ISMAEL M. C. <i....@fd...>]

Dear all,

I have a trouble when I submit a job which uses the transfer AFT file job. It uses a GASS (mode insecure) session. There are not problems with this session, since I am able to transfer files using the globus commands. Below is the log of gridsam.

2011-01-27 09:39:40,233 WARN  [UserMappingStage] You disabled security features: pool accounts and private workding directory.
2011-01-27 09:39:40,241 WARN  [UserMappingStage] Use the local user account (root) of gridsam to do jobs for user CN=gridsam
2011-01-27 09:39:40,460 INFO  [AbstractFileProviderSupport] SUBMIT Job
2011-01-27 09:39:40,481 INFO  [AFTFileTransferJob]  Transfer AFT File Job : 3F7944E207B98181095290B8BBF83F4F7839F11F start at 08:39:40    481  http://localhost:36199//opt/gridway/5.6.1//libexec/gw_wrapper.sh --> /root/workdir/a0/00/46/gridsam-ff8081812dc69192012dc6a0c164000a//opt/gridway/5.6.1//libexec/gw_wrapper.sh.wrapper retry time :0
2011-01-27 09:39:40,494 INFO  [HttpMethodBase] Recoverable exception caught when processing request
2011-01-27 09:39:40,495 WARN  [HttpMethodBase] Recoverable exception caught but MethodRetryHandler.retryMethod() returned false, rethrowing exception
2011-01-27 09:39:40,495 ERROR [TransferAgentFactory] source URI is not resolvable
org.apache.commons.vfs.FileSystemException: Could not connect to HTTP server on "localhost".
    at org.apache.commons.vfs.provider.http.HttpClientFactory.createConnection(HttpClientFactory.java:106)
    at org.apache.commons.vfs.provider.http.HttpFileProvider.doCreateFileSystem(HttpFileProvider.java:82)
    at org.apache.commons.vfs.provider.AbstractOriginatingFileProvider.findFile(AbstractOriginatingFileProvider.java:81)
    at org.apache.commons.vfs.provider.AbstractOriginatingFileProvider.findFile(AbstractOriginatingFileProvider.java:62)
    at org.apache.commons.vfs.impl.DefaultFileSystemManager.resolveFile(DefaultFileSystemManager.java:641)
    at org.apache.commons.vfs.impl.DefaultFileSystemManager.resolveFile(DefaultFileSystemManager.java:582)
    at org.icenigrid.gridsam.core.plugin.transfer.protocol.AbstractTransferAgent.getFileObject(AbstractTransferAgent.java:239)
    at org.icenigrid.gridsam.core.plugin.transfer.protocol.TransferAgentFactory.resolveSourceFile(TransferAgentFactory.java:168)
    at org.icenigrid.gridsam.core.plugin.transfer.protocol.TransferAgentFactory.<init>(TransferAgentFactory.java:120)
    at org.icenigrid.gridsam.core.plugin.transfer.provider.AFTFileTransferJob.execute(AFTFileTransferJob.java:131)
    at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
    at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:525)
Caused by: org.apache.commons.httpclient.HttpRecoverableException: org.apache.commons.httpclient.HttpRecoverableException: Error in parsing the status  line from the response: unable to find line starting with "HTTP"
    at org.apache.commons.httpclient.HttpMethodBase.readResponse(HttpMethodBase.java:1962)
    at org.apache.commons.httpclient.HttpMethodBase.processRequest(HttpMethodBase.java:2653)
    at org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:1087)
    at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:643)
    at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:497)
    at org.apache.commons.vfs.provider.http.HttpClientFactory.createConnection(HttpClientFactory.java:102)
    ... 11 more
2011-01-27 09:39:40,508 INFO  [FileProcessHelper] AFT File FAILED.Could not connect to HTTP server on "localhost".
2011-01-27 09:39:40,525 INFO  [job] ff8081812dc69192012dc6a0c164000a reason for failure: Could not connect to HTTP server on "localhost".
2011-01-27 09:39:40,525 INFO  [stats] ff8081812dc69192012dc6a0c164000a: pending@1296117580132 staging-in@1296117580450 failed@1296117580525 
2011-01-27 09:39:40,561 INFO  [JobCleanupListener] delete the temp dir for failed job ff8081812dc69192012dc6a0c164000a


The version of commons-httpclient.jar is the 2.0.2, however, I have tested other versions with similar results. I hope that someone could help me to fix this problem. 

Best regards.

Re: [gridsam-discuss] Security in GridSAM/BES

[I. M. C. <i....@fd...>]

Hi,

my apologizes, I forgot to remove the handlers in the client-side. Now
GridSAM works without authentication.

Then, I take up again the BES service. Thus, my server config about BES
is:

<service name="bes" provider="java:MSG" style="message" use="literal">
<wsdlFile>org/icenigrid/gridsam/resource/schema/wsdl/bes.wsdl</wsdlFile>
        <requestFlow>
            <!--<handler type="soapmonitor"/>-->
            <!--<handler
type="java:org.apache.ws.axis.security.WSDoAllReceiver">
                <parameter name="action" value="UsernameToken"/>
                <parameter name="passwordCallbackClass"
value="org.icenigrid.gridsam.bes.webservice.common.PWCallback"/>
            </handler>-->
        </requestFlow>
        <responseFlow>
            <!--<handler type="soapmonitor"/>-->
        </responseFlow>
        <parameter name="allowedMethods" value="*"/>
        <parameter name="scope" value="application"/>
        <parameter name="className"
value="org.icenigrid.gridsam.bes.webservice.axis.BasicExecutionServiceAxisImpl"/>
</service>

But the execution of the BESCreateActivity (without myproxy, similar to
GridSAMSubmit) shows:

$ java -cp .. GridSAMClient BESCreateActivity -s
http://localhost:8080/gridsam/services/bes?wsdl -j test.jsdl 

2010-12-13 16:38:06,170 FATAL [BESCreateActivity] (main:) unable to
create activity: java.lang.SecurityException: attempting to add an
object which is not an instance of java.security.Principal to a
Subject's Principal Set
2010-12-13 16:38:06,175 FATAL [BESCreateActivity] (main:) AxisFault
 faultCode:
{http://schemas.xmlsoap.org/soap/envelope/}Server.userException
 faultSubcode: 
 faultString: java.lang.SecurityException: attempting to add an object
which is not an instance of java.security.Principal to a Subject's
Principal Set
 faultActor: 
 faultNode: 
 faultDetail: 
	{http://xml.apache.org/axis/}hostname:mc01

I hope some glue to fix this problem. Regards.

On Mon, 2010-12-13 at 15:27 +0100, I. Marín Carrión wrote:
> Dear all,
> 
> In order to focus the problem, I have left for now the BES service (and
> my own BES clients) and now I am using the GridSAM service.
> 
> My intention is using the client without authentication. So, I have done
> the next changes.
> 
> In server-config.wsdd: I have disabled the section "<!-- GridSAM with
> OMII WS-Security -->" and enabled the section "without WS-Security".
> Also, I have set the property allowUnauthorised to true.
> 
> Also, I have deleted all lines about myproxy in the GridSAMSubmit.java.
> The new compiled jar is placed in webapps/gridsam/WEB-INF/lib and in
> client/lib.
> 
> Thus, when I execute the primes_file.pl demo I always get "Jobs
> outstanding: 10. Jobs completed: 0. Jobs failed: 0". This problem
> disappears enabling the security in server-config.wsdd (even if the new
> gridsam-client.jar is still present).
> 
> I hope any idea to fix this problem.
> 
> Best regards.
> 
> On Thu, 2010-12-09 at 14:05 +0000, Justin Bradley wrote:
> > Hi,
> > 
> > In webapps/gridsam/WEB-INF/classes/GridSAMService.properties you will find a property called allowUnauthorised.
> > Try setting this to be 'true', as it is 'false' by default.  Restart your container and see if this fixes your problem.
> > 
> > Regards,
> > 	Justin
> > 
> > 
> > On 9 Dec 2010, at 09:45, I. Marín Carrión wrote:
> > 
> > > Dear all,
> > > 
> > > this is a grid developer from Complutense University of Madrid, Spain. 
> > > 
> > > We are using GridSAM as testing platform for our BES clients. These
> > > clients do not use any authentication method (for now) and so we have
> > > disabled any security mechanism from GridSAM. Thus, we comment the
> > > section from server-config.wsdd where "<!-- BES with OMII WS-Security
> > > -->" and uncomment where "<!-- BES withOut OMII WS-Security +
> > > Username/Password -->", but commenting also in this section the next
> > > lines:
> > > 
> > > <!--<handler type="java:org.apache.ws.axis.security.WSDoAllReceiver">
> > >                <parameter name="action" value="UsernameToken"/>
> > >                <parameter name="passwordCallbackClass"
> > > value="org.icenigrid.gridsam.bes.webservice.common.PWCallback"/>
> > >            </handler>-->
> > > 
> > > 
> > > However, when I try to submit a job using my own client, this provides
> > > an security exception: "java.lang.SecurityException: attempting to add
> > > an object which is not an instance of java.security.Principal to a
> > > Subject's Principal Set", which is thrown by
> > > org/apache/axis/client/Call.invoke().
> > > 
> > > Therefore, Should I make some changes more to disable any security
> > > mechanism of GridSAM/BES?
> > > 
> > > Best regards.
> > > 
> > > 
> > > ------------------------------------------------------------------------------
> > > This SF Dev2Dev email is sponsored by:
> > > 
> > > WikiLeaks The End of the Free Internet
> > > http://p.sf.net/sfu/therealnews-com
> > > _______________________________________________
> > > GridSAM-Discuss mailing list
> > > Gri...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gridsam-discuss
> > 
> > --
> > Justin Bradley
> > Senior Software Consultant
> > jb...@ec...
> > OMII-UK / EPrints Services
> > Bay 22, 4067, B32
> > University of Southampton
> > 
> > 
> > 
> > 
> > 
> 
> 
> 
> ------------------------------------------------------------------------------
> Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL,
> new data types, scalar functions, improved concurrency, built-in packages, 
> OCI, SQL*Plus, data movement tools, best practices and more.
> http://p.sf.net/sfu/oracle-sfdev2dev 
> _______________________________________________
> GridSAM-Discuss mailing list
> Gri...@li...
> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss

Re: [gridsam-discuss] Security in GridSAM/BES

[I. M. C. <i....@fd...>]

Dear all,

In order to focus the problem, I have left for now the BES service (and
my own BES clients) and now I am using the GridSAM service.

My intention is using the client without authentication. So, I have done
the next changes.

In server-config.wsdd: I have disabled the section "<!-- GridSAM with
OMII WS-Security -->" and enabled the section "without WS-Security".
Also, I have set the property allowUnauthorised to true.

Also, I have deleted all lines about myproxy in the GridSAMSubmit.java.
The new compiled jar is placed in webapps/gridsam/WEB-INF/lib and in
client/lib.

Thus, when I execute the primes_file.pl demo I always get "Jobs
outstanding: 10. Jobs completed: 0. Jobs failed: 0". This problem
disappears enabling the security in server-config.wsdd (even if the new
gridsam-client.jar is still present).

I hope any idea to fix this problem.

Best regards.

On Thu, 2010-12-09 at 14:05 +0000, Justin Bradley wrote:
> Hi,
> 
> In webapps/gridsam/WEB-INF/classes/GridSAMService.properties you will find a property called allowUnauthorised.
> Try setting this to be 'true', as it is 'false' by default.  Restart your container and see if this fixes your problem.
> 
> Regards,
> 	Justin
> 
> 
> On 9 Dec 2010, at 09:45, I. Marín Carrión wrote:
> 
> > Dear all,
> > 
> > this is a grid developer from Complutense University of Madrid, Spain. 
> > 
> > We are using GridSAM as testing platform for our BES clients. These
> > clients do not use any authentication method (for now) and so we have
> > disabled any security mechanism from GridSAM. Thus, we comment the
> > section from server-config.wsdd where "<!-- BES with OMII WS-Security
> > -->" and uncomment where "<!-- BES withOut OMII WS-Security +
> > Username/Password -->", but commenting also in this section the next
> > lines:
> > 
> > <!--<handler type="java:org.apache.ws.axis.security.WSDoAllReceiver">
> >                <parameter name="action" value="UsernameToken"/>
> >                <parameter name="passwordCallbackClass"
> > value="org.icenigrid.gridsam.bes.webservice.common.PWCallback"/>
> >            </handler>-->
> > 
> > 
> > However, when I try to submit a job using my own client, this provides
> > an security exception: "java.lang.SecurityException: attempting to add
> > an object which is not an instance of java.security.Principal to a
> > Subject's Principal Set", which is thrown by
> > org/apache/axis/client/Call.invoke().
> > 
> > Therefore, Should I make some changes more to disable any security
> > mechanism of GridSAM/BES?
> > 
> > Best regards.
> > 
> > 
> > ------------------------------------------------------------------------------
> > This SF Dev2Dev email is sponsored by:
> > 
> > WikiLeaks The End of the Free Internet
> > http://p.sf.net/sfu/therealnews-com
> > _______________________________________________
> > GridSAM-Discuss mailing list
> > Gri...@li...
> > https://lists.sourceforge.net/lists/listinfo/gridsam-discuss
> 
> --
> Justin Bradley
> Senior Software Consultant
> jb...@ec...
> OMII-UK / EPrints Services
> Bay 22, 4067, B32
> University of Southampton
> 
> 
> 
> 
> 

Re: [gridsam-discuss] Security in GridSAM/BES

[I. M. C. <i....@fd...>]

Hi Justin,

this does not fix the problem.

In the meantime, I have taken a look to BasicExecutionServiceAxisImpl.java which is referred by server-config.wsdd: 
<parameter name="className" value="org.icenigrid.gridsam.bzs.webservice.axis.BasicExecutionServiceAxisImpl"/>

In this class, I find that this service use X.509 certificates. In my
case, I should not use certificates, or any other authentication method.
Thus, I wonder if this functionality is actually disabled when I comment
the lines "<!-- BES with OMII WS-Security
> > -->" in server-config.wsdd. 

In fact, this class imports javax.security.auth.Subject, the package
that I now guess, causes the exception "java.lang.SecurityException:
attempting to add an object which is not an instance of
java.security.Principal to a Subject's Principal Set".

My apologizes if in the previous mail I have not explained well my
problem.

Best regards.


On Thu, 2010-12-09 at 14:05 +0000, Justin Bradley wrote:
> Hi,
> 
> In webapps/gridsam/WEB-INF/classes/GridSAMService.properties you will find a property called allowUnauthorised.
> Try setting this to be 'true', as it is 'false' by default.  Restart your container and see if this fixes your problem.
> 
> Regards,
> 	Justin
> 
> 
> On 9 Dec 2010, at 09:45, I. Marín Carrión wrote:
> 
> > Dear all,
> > 
> > this is a grid developer from Complutense University of Madrid, Spain. 
> > 
> > We are using GridSAM as testing platform for our BES clients. These
> > clients do not use any authentication method (for now) and so we have
> > disabled any security mechanism from GridSAM. Thus, we comment the
> > section from server-config.wsdd where "<!-- BES with OMII WS-Security
> > -->" and uncomment where "<!-- BES withOut OMII WS-Security +
> > Username/Password -->", but commenting also in this section the next
> > lines:
> > 
> > <!--<handler type="java:org.apache.ws.axis.security.WSDoAllReceiver">
> >                <parameter name="action" value="UsernameToken"/>
> >                <parameter name="passwordCallbackClass"
> > value="org.icenigrid.gridsam.bes.webservice.common.PWCallback"/>
> >            </handler>-->
> > 
> > 
> > However, when I try to submit a job using my own client, this provides
> > an security exception: "java.lang.SecurityException: attempting to add
> > an object which is not an instance of java.security.Principal to a
> > Subject's Principal Set", which is thrown by
> > org/apache/axis/client/Call.invoke().
> > 
> > Therefore, Should I make some changes more to disable any security
> > mechanism of GridSAM/BES?
> > 
> > Best regards.
> > 
> > 
> > ------------------------------------------------------------------------------
> > This SF Dev2Dev email is sponsored by:
> > 
> > WikiLeaks The End of the Free Internet
> > http://p.sf.net/sfu/therealnews-com
> > _______________________________________________
> > GridSAM-Discuss mailing list
> > Gri...@li...
> > https://lists.sourceforge.net/lists/listinfo/gridsam-discuss
> 
> --
> Justin Bradley
> Senior Software Consultant
> jb...@ec...
> OMII-UK / EPrints Services
> Bay 22, 4067, B32
> University of Southampton
> 
> 
> 
> 
> 

-- 
I. Marín Carrión

DSA Research Group:  http://dsa-research.org
Complutense University of Madrid

Re: [gridsam-discuss] Security in GridSAM/BES

[Justin B. <jb...@ec...>]

Hi,

In webapps/gridsam/WEB-INF/classes/GridSAMService.properties you will find a property called allowUnauthorised.
Try setting this to be 'true', as it is 'false' by default.  Restart your container and see if this fixes your problem.

Regards,
	Justin


On 9 Dec 2010, at 09:45, I. Marín Carrión wrote:

> Dear all,
> 
> this is a grid developer from Complutense University of Madrid, Spain. 
> 
> We are using GridSAM as testing platform for our BES clients. These
> clients do not use any authentication method (for now) and so we have
> disabled any security mechanism from GridSAM. Thus, we comment the
> section from server-config.wsdd where "<!-- BES with OMII WS-Security
> -->" and uncomment where "<!-- BES withOut OMII WS-Security +
> Username/Password -->", but commenting also in this section the next
> lines:
> 
> <!--<handler type="java:org.apache.ws.axis.security.WSDoAllReceiver">
>                <parameter name="action" value="UsernameToken"/>
>                <parameter name="passwordCallbackClass"
> value="org.icenigrid.gridsam.bes.webservice.common.PWCallback"/>
>            </handler>-->
> 
> 
> However, when I try to submit a job using my own client, this provides
> an security exception: "java.lang.SecurityException: attempting to add
> an object which is not an instance of java.security.Principal to a
> Subject's Principal Set", which is thrown by
> org/apache/axis/client/Call.invoke().
> 
> Therefore, Should I make some changes more to disable any security
> mechanism of GridSAM/BES?
> 
> Best regards.
> 
> 
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--
Justin Bradley
Senior Software Consultant
jb...@ec...
OMII-UK / EPrints Services
Bay 22, 4067, B32
University of Southampton

[gridsam-discuss] Security in GridSAM/BES

[I. M. C. <i....@fd...>]

Dear all,

this is a grid developer from Complutense University of Madrid, Spain. 

We are using GridSAM as testing platform for our BES clients. These
clients do not use any authentication method (for now) and so we have
disabled any security mechanism from GridSAM. Thus, we comment the
section from server-config.wsdd where "<!-- BES with OMII WS-Security
-->" and uncomment where "<!-- BES withOut OMII WS-Security +
Username/Password -->", but commenting also in this section the next
lines:

<!--<handler type="java:org.apache.ws.axis.security.WSDoAllReceiver">
                <parameter name="action" value="UsernameToken"/>
                <parameter name="passwordCallbackClass"
value="org.icenigrid.gridsam.bes.webservice.common.PWCallback"/>
            </handler>-->


However, when I try to submit a job using my own client, this provides
an security exception: "java.lang.SecurityException: attempting to add
an object which is not an instance of java.security.Principal to a
Subject's Principal Set", which is thrown by
org/apache/axis/client/Call.invoke().

Therefore, Should I make some changes more to disable any security
mechanism of GridSAM/BES?

Best regards.

[gridsam-discuss] GridSAM 2.3.0 released

[Justin B. <j.b...@om...>]

Hi All,

We are pleased to announce the release of GridSAM 2.3.0.
This release represents the output from the first of the 2.3.x series of developer releases.

The focus of this release was to make GridSAM stand independently from the OMII-UK Campus Grid Toolkit.

With this in mind, the client distribution now comes as a simple zip file. Besides GridSAM this contains parts of the OMII-UK CGT client and a selection of the examples and demonstrations previously found in CGT.  This client zip can simply be unpacked and used.

The service now comes as a single war file, which can be deployed easily, and is configured by default to run jobs locally.  Some familiar configuration tools have been added from CGT as well as some support libraries.

See the new installation quickstart guide on how to get started.

The service can now be deployed multiple times within the same container, as all its configuration information and dependencies are contained within the local web application.
This allows for different endpoints to be configured within the same container to submit to different backend compute resources.

Further support for JSDL resources have also been added.

See SourceForge for the file releases, https://sourceforge.net/projects/gridsam/files/

Regards,
	Justin

--
Justin Bradley
Senior Software Consultant
j.b...@om...
OMII-UK / EPrints Services
Bay 22, 4067, B32
University of Southampton

[gridsam-discuss] GridSAM 2.2.0 released

[Justin B. <j.b...@om...>]

Hi All,

We are pleased to announce the release of GridSAM 2.2.0.
This release represents the output from the 2.1.x series of develop releases.

See SourceForge for the file releases, https://sourceforge.net/projects/gridsam/files/

Here is a brief list of the main changes to GridSAM 2.2, since the release of 2.0.
For a more complete list, please see
https://sourceforge.net/projects/gridsam/files/gridsam/2.2.0/GridSAM-2.2.0-changes-overview.txt/view

New DRM connectors, more configurable and complete than their predecessors
	- PBS
	- Condor
	- LSF
	- Sun Grid Engine

Updated existing DRM connectors
	- Globus
	- Local execution (fork)

Interoperability and standards compliance
	- OGSA BES version 1.0
	- HPC Basic Profile version 1.0	
	- JSDL HPC Profile Application Extension version 1.0
	- HPC File Staging Profile version 1.0
	- HPC Common Case Profile: Activity Credential version 0.1
	- JSDL SPMD version 1.0

Asynchronous and reliable data transfer mechanisms
	- This reduces bottlenecks in data transfers and increases their reliability by retrying failed transfers.

User management
	- Allows jobs to be submitted as the user that owns it, rather than as the user the container is running as.

Reworked internals
	- Much of the internals of GridSAM has been refined to allow for more efficient job management, allowing for higher throughput and system uptime.

Upgraded version of third party libraries
	- Quartz moved from 1.4.5 to 1.6.5
	- Globus COG Kit moved from 1.2.0 to 1.6.0

Regards,
	Justin

--
Justin Bradley
Senior Software Consultant
j.b...@om...
OMII-UK / EPrints Services
Bay 22, 4067, B32
University of Southampton

[gridsam-discuss] GridSAM 2.1.10 released

[Justin B. <j.b...@om...>]

Hi All,

We are pleased to announce the release of GridSAM 2.1.10.

This release focuses on better supporting existing platforms.
Here follows a brief outline of the changes since 2.1.9.

- Improved support for Globus, The DRM connector has been overhauled and now supports asynchronous file transfer and has improved resource management.
- OGSA-BES GetFactoryAttributes supported.
- New Sun Grid Engine support added, bringing it inline with PBS and Condor DRM connectors.
- More efficient and more flexible DRM configurations.
- Addition of new customisable file transfer routines, to allow for the integration of local bespoke data staging services.

For a complete list of changes, see the change log
https://sourceforge.net/projects/gridsam/files/gridsam/2.1.10/GridSAM-2.1.10-Change-Log.txt/view

This release of GridSAM is also likely to be the last in this development series.
GridSAM 2.2.0 will be released shortly.
Further development items will be applied to GridSAM 2.3.x.

Regards,
	Justin

--
Justin Bradley
Senior Software Consultant
j.b...@om...
OMII-UK / EPrints Services
Bay 22, 4067, B32
University of Southampton

[gridsam-discuss] GridSAM - A plan for July 2010

[Justin B. <j.b...@om...>]

Hi All,

July 2010 has been set aside for further GridSAM development.
There are 5 main things to achieve in this timeframe.  Anything that does not get completed will be addressed over the following weeks as time permits.
Items 1, 2 and 3 will be performed in sequence, while Item 4 will be done in parallel with these and item 5 performed last.

1) Resolve the outstanding GSIFTP issue that results in resource leaks from within the Globus COG kit.

Some headway has been made already with this, with the infrastructure in place to take the handlers for transferring files out of process (so a short lived process is spawned to service the transfer).
This will take up to 1 week to complete.

2) Round off the 2.1.x development series. release 2.2.0 and move to a 2.3.x development series.

2.1.x will be renamed to 2.2.0 and a subversion branch made for this. 2.2.0 will be considered stable and will be released.  No more development will happen under the 2.1.x banner, any bug fixes will be made on the 2.2.x branch.
2.3.x will be the new version scheme adopted by the trunk. New development versions will be based upon this.
This will take up to a day to complete.

3) Decouple GridSAM from the OMII-UK Campus Grid Toolkit (CGT).

- Import the configuration scripts and demonstrators from CGT into the GridSAM codebase.
- Repackage the client so it can be shipped as a single zip file, which can just be unpacked and used.
- Repackage the server so it can be shipped as single war file.
This will take  between 2 and 3 weeks to complete.

4) JSDL Resources support for ICT PBS DRM connector.

This will be done within the above time frame.  The changes will be committed to the trunk and therefore will appear in the development series in use at that time.
This is a well understood piece of work that will propagate JSDL Resource specifications through to the PBS resource manager back-end.
This will take up to 1 week to complete.

5) Implement LCAS/LCMAPS integration.

This will be begun within the above time frame, although may extend into August.  The changes will be committed to the trunk and therefore will appear in the development series in use at that time.
Currently in discussions with NGS personnel (who have deployed and use LCAS/LCMAPS) to validate our implementation plan; time estimates will be made available in due course.


For the latest version of this document, please see
http://downloads.sourceforge.net/project/gridsam/project-docs/GridSAM-July2010.txt

--
Justin Bradley
Senior Software Consultant
j.b...@om...
OMII-UK / EPrints Services
Bay 22, 4067, B32
University of Southampton

Re: [gridsam-discuss] How to install GridSAM alone

[Justin B. <j.b...@om...>]

Hi Hailong,

Thank you for your enquiry.
There is currently no explicit documentation on how to achieve what you want.

However, it is entirely possible to install GridSAM in an existing container, although its only really been attempted for Tomcat.
Which container are you intending to use?
Also the preferred database back-end is MySQL, although other systems could be made to work quite easily.

We have an intention to work on some issues which are likely to help you though.
Over the next few weeks the plan is to repackage GridSAM so that it comes as a war file, so it can be more easily deployed within existing systems.
Then, the configuration scripts that currently come with other OMII software would be made part of the GridSAM webapp.

Regards,
	Justin

On 21 Jun 2010, at 02:54, hailong.yang1115 wrote:

> Dear all,
>  
> Is there a guide about how to install GridSAM alone? We don't want to install all stuffs packed in OMII-server since we alreay have some pre-installed such as web container and database.
>  
> Any help will be appreciated.
>  
> Hailong
>  
> 2010-06-21
> ***********************************************
> * Hailong Yang, PhD. Candidate 
> * Sino-German Joint Software Institute, 
> * School of Computer Science&Engineering, Beihang University
> * Phone: (86-010)82315908
> * Email: hai...@gm...
> * Address: G413, New Main Building in Beihang University, 
> *              No.37 XueYuan Road,HaiDian District, 
> *              Beijing,P.R.China,100191
> *********************************************** 
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate 
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the 
> lucky parental unit.  See the prize list and enter to win: 
> http://p.sf.net/sfu/thinkgeek-promo_______________________________________________
> GridSAM-Discuss mailing list
> Gri...@li...
> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss

--
Justin Bradley
Senior Software Consultant
j.b...@om...
OMII-UK / EPrints Services
Bay 22, 4067, B32
University of Southampton

[gridsam-discuss] How to install GridSAM alone

[hailong.yang1115 <hai...@gm...>]

Dear all,

Is there a guide about how to install GridSAM alone? We don't want to install all stuffs packed in OMII-server since we alreay have some pre-installed such as web container and database.

Any help will be appreciated.

Hailong

2010-06-21 



***********************************************
* Hailong Yang, PhD. Candidate 
* Sino-German Joint Software Institute, 
* School of Computer Science&Engineering, Beihang University
* Phone: (86-010)82315908
* Email: hai...@gm...
* Address: G413, New Main Building in Beihang University, 
*              No.37 XueYuan Road,HaiDian District, 
*              Beijing,P.R.China,100191
*********************************************** 

[gridsam-discuss] GridSAM in use at the Irish Centre for High End Computing

[Tim P. <ts...@ec...>]

GridSAM is now being used by the Irish Bioportal project to allow
bioinformaticians to submit jobs to computational clusters at the
Irish Centre for High End Computing (ICHEC).

OMII-UK engineers extended GridSAM's SSH authentication mechanism
to fit the access policy required by ICHEC.

The OMII-UK Newsletter article is online at http://www.omii.ac.uk/wiki/Nwsltr0310BioPortal

The BioPortal project page is at  http://www.ichec.ie/research/irish_bioportal_project

The ICHEC front page is at www.ichec.ie<http://www.ichec.ie/>


Tim Parkinson
Project Manager
OMII-UK
University of Southampton

[gridsam-discuss] GridSAM mailing list management

[Justin B. <jb...@ec...>]

Hi All,

Given the low level of traffic to the two GridSAM mailing lists, I am going to move over to a single list from now on.
There is currently no real benefit in having 2 lists.

gridsam-discuss has 45 members and gridsam-developer has 22.  Of the 22 only 5 are not also members of gridsam-discuss.
Therefore I'm going to subscribe these five members to gridsam-discuss and stop posts to gridsam-developer.

Regards,
	Justin

--
Justin Bradley
Senior Software Consultant
j.b...@om...
OMII-UK
Bay 23, 4067, B32
University of Southampton