[kepler-users] Socket streaming in Kepler

[Matt Jones]

Nachiket,

Is the jar file you are trying to execute a Kepler instance?  If so, you
should probably use the shell script that we've developed which allows you
to pass in kar files.

https://kepler-project.org/developers/reference/executing-kepler-from-the-command-line

Matt

On Tue, May 8, 2012 at 1:31 AM, Nachiket Kate <
nachiket_kate at persistent.co.in> wrote:

> 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
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