[Bioclusters] anyone using gridMathematica ?

[Joe Landman]

Chris Dagdigian wrote:

...

> This is not optimal because the gridMathematica job will still launch 
> and run outside the control of the cluster scheduler and resource 
> management layers. On the plus side however we at least allow for the 
> cluster software to make informed decisions on which nodes the math jobs 
> run on.


This is the scheduler bubble I indicated.  It is not so hard to launch 
an MPI job where all it does is "sleep" in a loop.  Then you have your 
list of machines from the DRM, and can launch in there.  The bubble is 
hard on the DRM as you are effectively requesting a static resource in 
the middle of your dynamic system.  They often do not play well together.

 From SGE, I use the mpich parallel environment to get the machine file 
to be autogenerated

	q{sub,rsh,...} -pe mpich N ...

Then you have $TMPDIR/machines available to pull out the machines file. 
  I am sure a similar "trick" exists under LSF (though as I do not have 
it on my machines at the moment, I cannot tell you what it is).

There are other techniques, and just like these others, they are hacks. 
  But some of them work, so those are good....

-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615