[kepler-users] Socket streaming in Kepler

[Nachiket Kate]

Hi,

Thanks Christopher for BCVTB.
I have another doubt regarding "JobCreator" actor in kepler.
I would like to run a java jar with certain parameters (inputs to java jar) as a job on SGE,

e.g.   java  -Xmx1024m -jar abc.jar -inputdir "some path" -outputdir "some path"

for this, I have provided the path of executable jar(here abc.jar) in JobCreator's executable file field. This scenario works well if I didn't provide jar parameters i.e. inputdir and outputdir but with these parameters it's not working.
Is there any solution available for such scenarios?

~Nachiket

-----Original Message-----
From: Christopher Brooks [mailto:cxh at eecs.berkeley.edu] 
Sent: Friday, May 04, 2012 8:58 PM
To: Nachiket Kate
Cc: Michal Owsiak; Matt Jones; kepler-users at kepler-project.org
Subject: Re: [kepler-users] Socket streaming in Kepler

Hi Nachiket,
Kepler uses Ptolemy II as its engine.
The Ptolemy II devel tree includes the Building Controls Virtual Test Bed (BCVTB, http://simulationresearch.lbl.gov/bcvtb), which includes a way to communicate subprocesses via BSD sockets or via the command line.  There is a paper at http://dx.doi.org/10.1080/19401493.2010.518631.

I'm unsure of what you mean by "socket streaming" and whether this would be compatible with the type of sockets used in BCVTB.  If you are interested, the thing to do would be to look at the paper and then download BCVTB and see if it meets your needs.  Getting BCVTB visible within Kepler could be as simple as building Kepler using the devel tree and possibly editing a few files so that ptII/lbnl is not excluded from the build.  It may also be necessary to run configure and make.

_Christopher

On 5/4/12 1:16 AM, Nachiket Kate wrote:
> Hi Michal,
>
> We have a bioinformatics pipeline and we need a streaming support for 
> running its steps through socket streaming so is there any module or add-on which we can use for our project or do we need to develop our own actors for the same?
>
> Nachiket
>
> -----Original Message-----
> From: Michal Owsiak [mailto:michal.owsiak at man.poznan.pl]
> Sent: Friday, May 04, 2012 11:35 AM
> To: Nachiket Kate
> Subject: Socket streaming in Kepler
>
> Hello Kate,
>
> are you referring to Serpens suite that can be found here:
>
> http://scilla.man.poznan.pl:8080/confluence
>
> Or do you have something else in mind?
>
> Michal
>
> --
> Michal Owsiak<michal.owsiak at man.poznan.pl>
>
> Institute of Bioorganic Chemistry PAS
> Poznan Supercomputing and Networking Center Noskowskiego 12/14, 61-704 
> Poznan, POLAND
>
> http://www.man.poznan.pl
>
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-- 
Christopher Brooks, PMP                       University of California
CHESS Executive Director                      US Mail: 337 Cory Hall
Programmer/Analyst CHESS/Ptolemy/Trust        Berkeley, CA 94720-1774
ph: 510.643.9841                                (Office: 545Q Cory)
home: (F-Tu) 707.665.0131 cell: 707.332.0670


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