[Bioclusters] gridMathematica and bioinformatics

Andrew Fant bioclusters@bioinformatics.org
Wed, 22 Oct 2003 11:38:22 -0400

Quoting "Andrew A. de Laix" <delaix@wolfram.com>:

> Dear Mr. Dagdigian,
> 	I am doing research on how Mathematica is used in biology, and I
> stumbled across an email exchange you had on the bioclusters email
> list
> about gridMathematica.  Firstly, where you successful in getting
> gridMathematica to run satisfactorily?  I would be interested in
> knowing how
> you have been applying Mathematica and gridMathematica to
> bioinformatics and
> related problems.  What features did you find useful?  How can we
> make it
> easier to use Mathematica and gridMathematica?  What features would
> you like
> to see in future versions of Mathematica and gridMathematica?  

     I was the project lead on the project that Chris referenced in the
posting you were referencing.   At the moment, we don't have any
biology-specific applications of Mathematica in use or under
development.  The issue we are running into with GridMathematica has to
do with the mechanism of spawning slave processes.  At present, the
software appears to be designed to require users to specify what hosts
to spawn processes on. Are there any plans to allow people using
GridMathematica in a scheduler/batch driven cluster to request some sort
of node list from the scheduler?  We have a work-around that uses shell
scripts and cut and paste, but that exposes a lot more of the internal
workings of the cluster to the end-users than anyone here is comfortable

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