[kepler-users] Sample workflow using JobSubmission/JobManager

Thu Nov 1 17:12:38 PDT 2012

Hi Eduardo,

     If you start kepler from kepler.sh/kepler.bat, not double-clicking 
kepler icon, a console will show up and it normally has more information 
on errors.

     I checked the '-M' option of ssh and the implementation of ssh 
related code in Kepler. I don't think Kepler supports control master. I 
also don't see the Jsch library we used for ssh actors support it. So 
it's hard for us to update our code to do it.

     But I think there is still one way workaround. How do you set up 
the ssh connection at the first place? Type your two passwords in 
command line? Does it work if you try it in Kepler using 'SSH Session' 
actor? The same ssh session actor generated by the 'SSH Session' actor 
can be postponed and shared by other workflow executions within the same 
JVM. To do it, the parameter 'postpone' of the actor has to be selected 
(true) and the 'closeAtEnd' has to be false. So if you split the 
workflow into two workflows. The first workflow only has 'Host' and 'SSH 
Session'. The second one has other parts. If you can generate correct 
ssh session using the first workflow. You can run the second workflow 
many times without creating new ssh sessions. My tests work here.

     I'm ccing the email to Norbert. He is the original developer of the 
actors and workflows. He might have better solutions for you.

Best wishes

Sincerely yours

Jianwu Wang, Ph.D.
jianwu at sdsc.edu
http://users.sdsc.edu/~jianwu/

Assistant Project Scientist
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.

On 11/1/12 2:08 PM, Valente, Eduardo G. (GSFC-610.3)[GLOBAL SCIENCE & 
TECHNOLOGY INC] wrote:
> The failure is graceful in that the session return true for the failed 
> port.  If there is a way to view logs for that actor please let me know.
>
> Two factor authentication is the use of two passwords in the admission 
> process one of which utilizes an RSA token (changes every 30 seconds 
> or so).
>
> This means that it becomes impractical to automate processes if every 
> time we ssh the password is different.  And this two factor 
> authentication cannot be bypassed with public keys (otherwise known as 
> passwordless ssh).  The only option left is to use an existing ssh 
> connection enabled as the control master. Generally the –M switch of 
> ssh clients.  But it would appear the java ssh client and the system 
> ssh client do not "see" each other.  If that is the case than the java 
> version would need such a mode as well.  Currently I see two modes: 
> interactive with password request and passwordless with identity file.
>
> I cannot otherwise provide you a means to recreate the environment we 
> have.  But look into the concept of control master and you will be 
> able to investigate this possibility with the ssh session actor.
>
> Thanks,
> Eduardo
>
> From: Jianwu Wang <jianwu at sdsc.edu <mailto:jianwu at sdsc.edu>>
> Date: Thursday, November 1, 2012 4:52 PM
> To: "Valente, Eduardo G. (GSFC-610.3)[GLOBAL SCIENCE & TECHNOLOGY 
> INC]" <eduardo.g.valente at nasa.gov <mailto:eduardo.g.valente at nasa.gov>>
> Cc: "kepler-users at kepler-project.org 
> <mailto:kepler-users at kepler-project.org>" 
> <kepler-users at kepler-project.org <mailto:kepler-users at kepler-project.org>>
> Subject: Re: [kepler-users] Sample workflow using JobSubmission/JobManager
>
> Hi Eduardo,
>
>     So you failed even just using 'SSH Session' actor? Did you get any 
> error or exception message? It's new to me for the two-factor 
> authentication. If you tell me how to reproduce it, I can dig into it 
> and check what went wrong.
> Best wishes
>
> Sincerely yours
>
> Jianwu Wang, Ph.D.
> jianwu at sdsc.eduhttp://users.sdsc.edu/~jianwu/
>
> Assistant Project Scientist
> Scientific Workflow Automation Technologies (SWAT) Laboratory
> San Diego Supercomputer Center
> University of California, San Diego
> San Diego, CA, U.S.A.
> On 11/1/12 1:45 PM, Valente, Eduardo G. (GSFC-610.3)[GLOBAL SCIENCE & 
> TECHNOLOGY INC] wrote:
>> Thanks.  The workflow crashes kepler at a "type detection" step.  So 
>> I am trying just the SSH session step for starters.  I am running in 
>> an environment with two-factor authentication.  So I authenticate ssh 
>> with control master enabled hoping that subsequent ssh attempts by 
>> kepler use the existing open connection. At the kepler workflow I set 
>> up the ssh session with an identity file hoping it would use the 
>> control master session, but it is failing to do so.  Any thoughts on 
>> this mode of operation?
>> Eduardo
>>
>> From: Jianwu Wang <jianwu at sdsc.edu <mailto:jianwu at sdsc.edu>>
>> Date: Wednesday, October 31, 2012 5:50 PM
>> To: "Valente, Eduardo G. (GSFC-610.3)[GLOBAL SCIENCE & TECHNOLOGY 
>> INC]" <eduardo.g.valente at nasa.gov <mailto:eduardo.g.valente at nasa.gov>>
>> Cc: "kepler-users at kepler-project.org 
>> <mailto:kepler-users at kepler-project.org>" 
>> <kepler-users at kepler-project.org 
>> <mailto:kepler-users at kepler-project.org>>
>> Subject: Re: [kepler-users] Sample workflow using 
>> JobSubmission/JobManager
>>
>> Hi Eduardo,
>>
>>     A sample workflow using JobSubmission/JobManager can be found at 
>> https://code.kepler-project.org/code/kepler/trunk/workflows/SC06-Tutorial/JobSubmission.xml. 
>> To use it in PBS environment,  you just need to edit the 'JobManager' 
>> parameter to be 'PBS'. Other parameters such as 'SimTarget' and 
>> 'JobScript' also need to be configured to fit your information.
>> Best wishes
>>
>> Sincerely yours
>>
>> Jianwu Wang, Ph.D.
>> jianwu at sdsc.eduhttp://users.sdsc.edu/~jianwu/
>>
>> Assistant Project Scientist
>> Scientific Workflow Automation Technologies (SWAT) Laboratory
>> San Diego Supercomputer Center
>> University of California, San Diego
>> San Diego, CA, U.S.A.
>> On 10/31/12 2:22 PM, Valente, Eduardo G. (GSFC-610.3)[GLOBAL SCIENCE 
>> & TECHNOLOGY INC] wrote:
>>> Does anyone have a sample workflow that exercises a PBS based HPC 
>>> environment that they would like to share?
>>> Thanks.
>>>
>>>
>>>
>>> _______________________________________________
>>> Kepler-users mailing list
>>> Kepler-users at kepler-project.orghttp://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>
>

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