Help for submit job on cluster

[Azir Aliu]

Hi,
My name is Azir, I'm PhD student on Bioinformatics, I used the ImageJ and I
and my mentor, we are egregious from this tool. But know we like to send the
job on GRID. But I'm not sow familiar and I have a lot of problems, I
downloaded the headless.jar and now I don't have idea what's next. If you
have submitted sum job Please give me the example, But please let be step by
step (for unfamilary users). Thank a lot.
Azir

[Albert Cardona]

Azir,

I have no experience with your kind of cluster, but the essentials are
these:

- in the ImageJ classpath, place the headless.jar before the ij.jar

- try it out first with a simple task; if it fails, you may need a
virtual frame buffer (Xvfb)
  To set it up: lauch Xvfb with any number as argument and in the
background like this:

Xvfb :15 &

   then lauch ImageJ with that DISPLAY value:

DISPLAY=:15 java -classpath headless.jar:ij.jar ij.ImageJ -batch
/path/to/plugin_launcher_macro.txt


And please read ALL the documentation regarding your cluster submission
scripts, and the Xvfb, which is accessible using the 'man' command.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[dscho]

Hi,

On Fri, 19 Oct 2007, Azir Aliu wrote:

> My name is Azir, I'm PhD student on Bioinformatics, I used the ImageJ
> and I and my mentor, we are egregious from this tool. But know we like
> to send the job on GRID. But I'm not sow familiar and I have a lot of
> problems, I downloaded the headless.jar and now I don't have idea what's
> next. If you have submitted sum job Please give me the example, But
> please let be step by step (for unfamilary users).

A lot really depends on your specific cluster setup (cluster in the common
sense; not the Microsoft one which tries to redefine "cluster" to mean
"hot standby").

For example, if your cluster relies on MPI you need to adapt your plugins
to make use of that.  I am just about to set up something like this, using
mpiJava (even if there is MPJ, I hear, which does not need JNI, and is
therefore easier to install).

But there are a lot of different cluster setups out there, some as simple
as using ssh to distribute jobs, some very sophisticated, trying to
imitate a single multi-core processor.

So it really depends.  Without more information from your side, I am
afraid there is nothing I can do to help.

Ciao,
Dscho

[Mikhail Umorin]

Azir --

Are you talking about SunGrid? I have some experience with that, so I may be
able to help you. Please, be specific.

Mikhail.
On Fri October 19 2007, Azir Aliu wrote:
> Hi,
> My name is Azir, I'm PhD student on Bioinformatics, I used the ImageJ and I
> and my mentor, we are egregious from this tool. But know we like to send
> the job on GRID. But I'm not sow familiar and I have a lot of problems, I
> downloaded the headless.jar and now I don't have idea what's next. If you
> have submitted sum job Please give me the example, But please let be step
> by step (for unfamilary users). Thank a lot.
> Azir

[Azir Aliu]

Tnank yoou very much, I will prove.
Regards,
Azir