[Bioperl-l] RE: bioperl pipeline picking momentum

[Aaron J Mackey]

In our experience PVFS is not vastly superior even to NFS, but that's just
our experience (and possibly our fault for not having things well
optimized to PVFS-based work, while having lived in an NFS-world for
sometime now).

-Aaron

On Fri, 12 Apr 2002, Lenny Teytelman wrote:

> Lincoln,
>
> I know that the Clemson cluster will some time in the future have PVFS
> (Parallel Virtual File System) instead of NFS.  It should be vastly
> superior.
>
> See http://parlweb.parl.clemson.edu/pvfs/index.html
>
> Lenny
>
> -----------------------------
> Lenny Teytelman
> Cold Spring Harbor Laboratory
> 516-367-8864
> teytelma@cshl.org
>
> On Fri, 12 Apr 2002, Lincoln Stein wrote:
>
> > I just talked to a couple of people from AVAKI yesterday.  They claim that
> > their grid architecture has an advantage over GLOBUS because it incorporates
> > a virtual filesystem that grids out the data as well as the CPUs (and has
> > better performance than NFS).  Anyone have insight into these claims?
> >
> > Lincoln
> >
> > On Friday 12 April 2002 05:45, Larry Ang wrote:
> > > Elia,
> > >
> > > Very comprehensive plan. We will work together.
> > >
> > > Larry
> > >
> > > -----Original Message-----
> > > From: Elia Stupka [mailto:elia@fugu-sg.org]
> > > Sent: Friday, April 12, 2002 5:36 PM
> > > To: Bioperl
> > > Cc: Ensembl dev list; Prasanna R Kolatkar; Lai Loong Fong; Larry Ang
> > > Subject: bioperl pipeline picking momentum
> > >
> > >
> > > Dear all,
> > >
> > > just thought I would let you know that the effort to create a
> > > bioperl-pipeline based on extending and improving the already very capable
> > > ensembl-pipeline is well underway.
> > >
> > > Jer Ming Chia and Shawn Hoon have spent two useful weeks at Hinxton
> > > discussing with ensemblers the specs of the new pipeline, and have started
> > > coding it all up.
> > >
> > > Moreover over here in Singapore a few Institutes have taken interest in
> > > it, so we are likely to see a strong interest as well as broader set of
> > > coders working on the project.
> > >
> > > Some of the aims of the new pipeline as compared to the previous one are
> > > (in order of ease of achievement):
> > >
> > > 1)Making the system very flexible in terms of where the input data comes
> > > from and where the output results should be stored. This used to be all in
> > > one mysql db, now it should be able to come from anywhere provided
> > > adaptors are in place to communicate to the resource.
> > > [already underway]
> > >
> > > 2)Making the system less LSF dependent. As a first step we are starting to
> > > play with PBS both on an alpha cluster and Itanium cluster, and will code
> > > the modules needed to make it interact with PBS. PBS is free and thus if
> > > we can make it work stably it opens the pipeline for use to a much wider
> > > set of people, even for small multiprocessor systems.
> > > [will start next week]
> > >
> > > 3)Making the pipeline GRID aware. This means making the pipeline code talk
> > > to GLOBUS and being able to use within a local pipeline resources
> > > (data/cpu) available elsewhere seemlessly, or almost ;)
> > > [will start on this in a few weeks]
> > >
> > > 4)Taking advantage of the GRID-awareness to start reasoning in terms of
> > > allocating analysis runs according to where they are most suited or where
> > > there is more resources. In other words run cpu-intensive jobs on SNP
> > > systems, small-but-many jobs on MPP systems, and of course allocate "a la
> > > LSF" according to resources available.
> > > [wishful thinking?]
> > >
> > > Just thought I should let you know :)
> > >
> > > Elia
> >
>
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-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu